Notes on Note-keeping Software

YojimboSomehow, I’ve noticed, when someone brings up the subject of note-keeping software, it often turns into a much more extensive discussion than originally intended. Last Thursday I wrote about my search for the right all-purpose repository for recording details that would otherwise escape me, followed it up yesterday with some ruminations on the philosophical questions that search raises about online versus offline software, and now here I am again already, writing a third installment.

People come out of the woodwork with suggestions and opinions when it comes to this particular software niche. It’s been really helpful, so I felt it was my duty to report back on what I heard and what path I’ve decided to take.

Note Once, Review Anywhere

In particular, I heard a lot about Evernote, a very intriguing solution that allows multi-platform access to one’s data. Evernote comes in several flavors: browser, desktop and iPhone; all of your snippets are synchronized via the net so that they are available from any of those clients. It’s a great idea, and I’ve just downloaded it to start playing with it. At first blush, it looks more complicated and less elegant than I’m looking for, but I have to admit its comprehensive synching approach is extremely appealing.

Yojimbo Sync Error

Sync It Over

In fact, the idea of synchronization seems popular with lots of folks: being able to use a desktop application to access your data from multiple computers thanks to a net-based service like .Mac is a compelling compromise that has a lot of currency as we wait for a generation of solutions that truly integrates the best of desktop and online software. Which sort of goes to show you how powerful the synchronization concept is; in my opinion, .Mac’s ability to keep application data on multiple computers in sync — like most synching software today — is buggy, unreliable and inelegant. And yet, people still find it compelling. I know I do; I use .Mac’s for this service constantly, and as much as I hate it, I’d be lost without it.

Above: Sync you got all that? Absolute gibberish helpfully provided by .Mac’s synching services.

Which probably makes it no accident that for now I’ve decided to go with a desktop application that, yes, uses .Mac to synchronize my notes across computers: Bare Bones Software’s excellently named Yojimbo. It’s pretty much everything I want in that it lets me take notes very simply in a TextEdit-like environment, assign tags to those notes (and hints at pre-existing tags) and uses .Mac’s synching seamlessly. Or as seamlessly as that service will allow anyway. It doesn’t allow a Web-based view of that data in the way that Evernote does, unfortunately, but I’m pretty sure I don’t really need that.

And that’s all I have to say about note-keeping software for today.

  1. There is an application, WebJimbo that allows you to access your Yojimbo database through a browser, using your mac as a server. It’s not the best option, but it worked better than .Mac sync for accessing my Yojimbo notes elsewhere until I gave up. Might work for you.

  2. Note-taking software is a complex topic. I was a long-time DEVONthink user (with an occasional side-note of OmniOutliner and Circus Ponies Notebook). Yojimbo has always been much too slow on my old PowerBook. So is Eagle Filer. And so was KIT, now Together which in its latter incarnation doesn’t even support Tiger anymore.

    I needed something like DEVONthink because I was kind of a digital cluttermeleon for a long time, collecting PDFs and lot’s of WebArchives from all over the Web, thinking I’d one day have time to read them and/or might find them useful. But over the years the archive grew without being of substantial use. So I finally pulled the plug and threw it all out.

    That made good old (quick and nimble!) VoodooPad an option (again). For a long time I couldn’t figure out how to use the personal/desktop wiki concept for myself. But lately it is beginning to grow on me—a lot! So if your focus is on taking note instead of storing masses of PDFs and WebArchives, I recommend taking a look at VoodooPad.

  3. For simplicity, Yojimbo may be the way to go. But if you want a note-taking application that is extensible in many different ways, perhaps you should take a look at Tinderbox?

  4. Ah, the note-taking issue. Always a fun one. I have, and have used, DevonThink Pro, Yojimbo, VoodooPad, Evernote, and any number of others. Still trying for the solution that works.

    Frankly, one thing that always sticks in my head is the type of things Cory Doctorow pays attention to: formats. He’s generally paranoid about this sort of thing, so has kept to ASCII text for his notes. It’s simple, you can take it anywhere with you, and the format will not go out of fashion anytime soon. Consider it long-term security. Also, ASCII is wickedly easy to search.

    I am currently working out some kind of system using TextMate (or BBEdit) as the note-taking app, and doing the ASCII thing myself.

  5. I’ve used Yojimbo for a while but am making the switch to Together.

    I got frustrated by the lack of sub-folders in Yojimbo that made my notes and bookmarks messy after few weeks of use.

    Now my Together database is all neat, with sub-folders and all, and the best is that you can drag everything into Together to make consistent files (emails, address book cards, excel documents, HTML…). And you can edit them from Together!

  6. Dom Dibble suggests note-taking with Tinderbox , because Tinderbox is extensible in so any interesting directions.

    And Yojimbo is nice for simplicity, and syncing.

    That’s why Tinderbox comes with a free copy of Yojimbo!

  7. Finding the right note-taking program is a Quest that whispers promises of ultimate organization. An illusion of course, but like others, I’ve tried most of these programs.
    I always wind up back with my long-time default, SOHO Notes, for reasons that always elude me. Like Together, it lets you create nested folders, though now that it allows tags I find it faster to keep a flat hierarchy and just search.
    Can anyone make a strong case for why Yojimbo better. The Quest goes on…

  8. I’m obsessed with taking notes about any interesting conversation I have, lecture I attend or paper I read. For me, editing in Emacs was more important than being able to sync. With Per Sederberg, I built an ascii text plus database-backed Emacs mode (Freex mode) that has worked really well for keeping track of my 10,000+ fragments.

  9. I’m a fan (for the most part) of SOHO Notes (formerly StickyBrain, which was a much cooler name IMO) from Chronos. Yojimbo seemed much clunkier to me when I tried it, and less feature-rich. Frankly, I didn’t understand all the hype about Yojimbo after using SOHO Notes. So I’ve stuck with SOHO Notes.

    That said, Chronos has an annoying habit of coming out with frequent paid updates without fixing the glitches in the previous version. For example, I can’t get that blasted, annoying Downloads window to auto-hide, despite choosing that option in the preferences. (This same “feature” annoys me in Safari as well). Inquiries to the developer received an initial response, but ultimately no resolution.

    But now, surprise!, I can pay to get the new version of SOHO Notes – in which the Downloads window glitch may or may not have been fixed. One reason I upgraded to the prior version (v.6) was the ability to ditch that stupid Downloads window, which was proclaimed a new feature in v.6. WRONG!

    Performance can be slow as well.

    Those gripes aside, SOHO Notes is the best thing I’ve found to collect all my digital “stuff.”

  10. I used Evernote for a while on Windows but for some reason lapsed in my use quite some time ago.
    Over the past few months, with recent updates, I’ve become hooked on Google Notebook. It has a Firefox plugin that makes it ever present as long as I’m logged into my Google account.
    It’s very easy to use for note-taking while reading web pages, and a simple right-click or control click will save the selected text plus the link in your most recently used notebook, but allows you to easily move it to another notebook.
    Notebooks allow sections, tagging, commenting, formatting, export to Google Docs, all in a good, simple interface.

  11. I agree with you on Yojimbo! I love it because its so lightweight. While I’ve tried products like DevonThink, I find them to get in the way more than being helpful.

    I’ve been using Yojimbo for over 2 years and am pretty happy. Of course there are a few small things that would make me even happier…
    – I use Yojimbo for lots of list making (it beats managing text files in the Finder), so easy access to strikethrough and perhaps borrowing a few of the outlining ideas from OmniFocus/OmniOutliner…
    – And, I also dump a lot of code snippets in Yojimbo, so it’d be incredibly cool to have some syntax formatting, or at the least one-click access to fixed-width font formatting.

  12. Here’s a vote for Evernote. I love the crossplatform part of it the most. At work I’m forced to use Windows, at home I have Macs and everywhere else, I have my iPhone. With Evernote, my notes and web clippings are always available.

    On top of that, syncing works perfectly unlike the continual problems I had with .Mac.

  13. For me, the purpose of keeping notes in a single database was to make them easy to find and organize. Now that Macs have spotlight, I can use the OS file system to do that and keep my notes in whatever format I think is appropriate for the thought.

  14. I use Notebook, but I’ll be switching to something else, as a feature that used to work properly, that they acknowledge is a bug [clipping and annotating a url ignores the annotation you type in], will only be fixed in the next PAID update [they’ve put out a couple of free updates since I reported it.

  15. May seem chaotic to some, but all of my notes are in my gmail drafts folder. I’m used to the interface, and searching is simple.

  16. Your employer makes my notetaker, shifd. It’s made with Adobe AIR, which I know nothing about and don’t really care to, but I do know that it works swimmingly on my mac, my pc, on my phone and on my couch.

    That said, I’m still a disorganized scatterbrained slob. And I blame your employer. Despair…

  17. Everyone, who needs simple text notes should take a look at the free Notational Velocity. It’s unbeatable fast , encrypts on the fly and has an interface which couldn’t be any simpler, I guess.

  18. Try Freemind, a mind mapping software. Cross-platform, open source, free; it’s available at Sourceforge.
    I find that it works great for note taking: it has nice shortcuts so you can do everything using just the keyboard. And finally, I find that my ideas, or discussions during a meeting, usually pop up in the most chaotic way: and Freemind handles that very well. Try it 🙂

  19. As has been noted, many computer users have tried and discarded a large number of note-taking applications. I can’t even begin to list the programs I’ve downloaded from Version Tracker over the years – and I have used all of the ones other commenters have listed and then some.

    I finally settled on KIT a couple of years ago. KIT has now become Together and it has gotten better with the name change. I have set up F2 as my keyboard shortcut to clip highlighted text or URLs or images or just about anything. These clips get imported exactly as seen on the screen. I can then tag them, drop them into different folders (or use Smart Folders) and my digital life has never been easier.

    One thing that matters a lot to me is the responsiveness of the developer. Steve Harris (Together and Feeder) was quite quick in answering questions before I even bought the packages, a habit that has remained after the sales.

  20. I have tried most, on the PC I really preferred MS OneNote, but on the Mac I use Journler and I am really happy with it. There are a few things that are not perfect, integration to email being one (very important when taking meeting minutes) and Spotlight integration would be nice. But its the best I have tried.

  21. as far as software is concerned, i’ve tried everything from mac journal, journler, devonthink pro to smaller foot print software such as x pad, voodoopad and the like, but i also have to namedrop soho notes a my favorite note manager as well. nested folders, wide range of customization, integration with soho organizer/address book, web archive, smart folders, tabbed browsing, etc.

    yojimbo is a great program for lighter and more concise information as it doesnt’ quite carry the same level of flexibility, customization or integration as soho notes in my opinion. one thing soho notes lacks is it’s ability to integrate seamlessly with browsers other than safari. still works great for me.

  22. I’ve been through the full range of these and settled on a combo of them. There’s notes and there’s notes…

    I echo the comments above in preferring Together to Yojimbo for simple gather and move on type organisation. More features, more formats, and cheaper and the developer Steve Harris is both very accessible and keeps the updates coming.

    I use VoodooPad for project notes/database type operations which might require some output at some point. I like being able to quickly spit out a simple wiki website, fully linked up for others to use. I use this for teaching for example, my course notes, related pdfs and so on are all here and all communicable with a simple export command.

    DevonThinkProOffice….combined with a Fujitsu Scansnap minds particular databases, my accounts for example, all letters, statements from the bank, any forms submitted for tax etc.

  23. Sorry about my earlier post about Circus Ponies SW saying they wouldn’t fix my bug until the next paid version. I didn’t correctly remember the response they sent me, which was “it will be fixed sometime in the future”. Jayson as CP actually took the time to track link my post to the bug report I submitted 4 months ago. Evidently I am the only person who uses Notebook to save and annotate URLs. And evidently the bug will be fixed in the next version.

  24. I’ve been skimming trough this looking for my own note taking application. Hey maybe it’s time time for me to step up from TextEdit, right? I’m a bit of a cheapskate when it comes to applications like this so I was hoping that one of them would be free. I’m not sure where the line is exactly, maybe the under $40 applications will get a second look. I got excited by Tinderbox then I realized it was like $230. It seemed a bit overkill but at the same time strangely compelling. Something about it promised I would be able to discover hidden connections in my own writings. Who knows, I may be genius! Thanks for getting me to think about this need. I plan to do a exhaustive search of the free applications before I lay down any money. And what about this Mail app upgrade in Leopard, is anyone using it?

  25. I thought your co-workers at the New York Times just created an application that solves these problems you were talking about last week in your last post? – did you try that? just covered it. You should take a look.

  26. Here’s one from left field: I develop an app called Mental Case. It’s not a catch-all app like Yojimbo, nor a basic note repository. Mental Case is for storing short snippets, notes, and images. It captures this information very efficiently with hot keys, and even supports build in screen shots.

    But what makes Mental Case different to most other note taking apps is that it reminds you of your notes. If you are like me, you capture information, and forget you even have it. Mental Case reminds you of it, making the information much more useful.

  27. I can’t say enough good things about VoodooPad, it’s so flexible and easy. I’ve got a ton of stuff in it. The free form linking pages concept is really great. I can organize my info the way I want. I love that.

  28. Call me crazy, but for quick notes, I use IMAP email. I put tagwords in the subject (ie “to-do:”, “note:”, and filter on those words into folder/subfolders. It’s searchable, I can attach images, quickly dump my clipboard, etc, and my email is always up, so I don’t have to mess around with another client or site. Also cross-platform and exportable. Also use MoinMoin for more complex documentation, but that’s another story.

  29. A vote from this corner for MacJournal, which (not surprisingly) takes a journal-istic approach but works well as a notekeeper even without touching the blogging features. This from a happy customer for a few years, and only that — link.

  30. First off – on not being able to remember things: I can tell you with 100% certainty that this is due to having a child(ren) living in your house. It doesn’t matter if this is the best, most even-tempered, well-behaved prodigy in North America, this effect with show itself on every parent (that has some intelligence to begin with).

    Hiring a personal (preferrably childless) assistant of some sort is the only true solution. Software can help, but it will fall short of the total resolution that a functioning human will give you. (There are good seminal pieces on outsourced personal assistants at

    I use a combination of a tablet PC with me at all meetings, running OneNote.

    Key are:
    – the ability to leave my notes as handwritten ink (it’s MS’s special vector ink, not bitmaps)
    – the ability to search all text throughout the entire repository, whether ink, typed, in an embedded file, or (get this) *text in an image*. This means you can snap a webcam shot of the whiteboard and find the text later with search!
    – the ability to record both audio and video, while taking notes. If you want to hear what was said when you wrote something, it is all time-synchronized!
    – integrates with Outlook
    – always auto-saving with every stroke
    – many output options for sharing/email notes
    – multiple computers can have a note/binder/section open at once (I roam with my tablet and come back to a desktop)

    – the CaptureX ink pen can be used to write in paper notebooks. Later, the pen will synch the recorded ink strokes into OneNote(!) Here’s to hoping LiveScribe will build this function into their digital pen…

    The bad:
    – MS proprietary, not open (wish it were some XML type file – probably will be in the future)
    – Can’t be web-hosted (which is actually fine for the stated purposes)
    – It’s all in one giant file, which makes me very nervous

    BUT I am still forever searching for a more perfect setup. I am considering switching to EverNote…

  31. We’re working on a real study of this because it remains a very persistent problem in the information management space. One issue with these programs (I’ve looked at all of them) is that many of their “helpful” features intrude on the freedom of note taking. This is pencil and paper is so lovable. The main shortcoming of course is that it isn’t integrated into the digital world. Some noted the use of digital handwriting solutions but they are fairly clunky and don’t feel right either. Maybe real digital paper will be an answer. However the integration and software around taking action on notes and ideas is wide open.

  32. Thanks for addressing this. I just started freelancing and setting up all my admin tools has been quite a challenge. Lots of bad or buggy software out there, and you can’t really know that until you try to use it.

    Anyway, after some research I settled on TiddlyWiki for my notetaking – and back it up to TiddlySpot. It’s a bit of a learning curve, but so far it’s been very rewarding. Especially because *I* own the HTML file I write to, and can store it locally as well as on their servers.

  33. I’ve been using Yojimbo since September and I like it. It’s not perfect, but the encryption feature is very, very handy. The search feature works great so I never worry too much about overtly organizing my notes in any way. I Just create my note, add a few keywords, and I’m done.

  34. I use the simpliest one, with an .mac acount and with your email, you can create a draft email in your computer, it’s syncs with your other computers and also you can access to your drafts online, you can modify it and it’s syncs with all your computers, iphone, etc. I was looking for an app to do that but I can’t find it, for me the best way is drafts, I don’t know if it works with other IMAP email acounts.

  35. I just started using Evernote, and it’s amazing. The automatic OCR is a killer feature. It also has so many different interfaces: desktop, web, generic mobile, iPhone, and even IMAP; it’s amazing. The ability to email notes into notebooks, maintain multiple notebooks, save searches, and publicly publish notebooks – all combined, it’s an amazing system that is remarkably easy to use, considering the depth of its powerful features.

Thank you! Your remarks have been sent to Khoi.