Testing the Yojimbo Waters

Anyone using Yojimbo? I’d like to collect a lot of my notes and documents in a single database and I downloaded the trial. It seems like it’s going to do exactly what I need, but if anyone has any tips or tricks I’d appreciate it.

I’m currently trying to work my way through importing a bunch of bookmarks without doing it manually. If anyone has any thoughts on importing a csv of bookmarks into Yojimbo I’d appreciate that too.

I bought Yojimbo many, many years ago. I left it behind many years ago!

It didn’t keep up with changes to the Apple ecosystem, sync with iOS was virtually non-existent, and the Mac app just never developed.

I would recommend DevonThink instead.

I use Yojimbo as my personal database, and I also use it as a 1Password alternative. Okay, it doesn’t have many of the benefits that 1Password offers, but it’s rock solid—you’d expect nothing less from Bare Bones—and it lets me feel like I retain more control of my data. Encryption can be allocated item by item, so sensitive information like passport numbers, for example, can be safely stored. iPad synchronisation is pretty basic but it works, which makes your data readily available when you’re on the go. There’s also a BB hosted subscription service for keeping multiple Macs in sync.
I use DTPO for research, but Yojimbo is where my data lives. There is another thread on this forum about favourite apps and I chose OmniGraffle but, believe me, Yojimbo romps home in a very close second place.

How does DevonThink handle storing web items? Does it archive the whole site or just store a link? I think I prefer keeping web-based items lighter weight, I don’t really bookmark to archive stuff, just to find it later.

I’m basically looking for a good alternative to Evernote, the “notebooks” and “stacks” metaphor drives me crazy. I imagine it’s not actually slower than browsing folders in Finder, but it sure feels slow to me.

DevonThink can save a bookmark, a web archive, a Markdown version, or a decluttered Markdown version. It can also save a PDF of the site.

This is selectable upon each import, so you can choose the most appropriate format.

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I loved Yojimbo for many years. I still think it’s the most “Mac-like” app for taking notes and storing data. The best thing about it was that when capturing data with the hotkey, it would look at your clipboard before presenting you with a UI, and customize the UI for the data. It was fast, fit in perfectly with the Mac, and was rock-solid reliable.

But, time passed, things changed, the iPhone changed computing forever, and Yojimbo just didn’t keep up. it didn’t adopt a widescreen view, it didn’t offer iCloud sync, it didn’t have an iPhone app, it didn’t adopt the new UI widgets for the toolbar, it didn’t adopt Markdown, etc…. It still works, but it feels old and stagnate.

I’ve talked to the devs a few times, and they always give the same feedback. No future plans for an iPhone app. No plans to change anything, just to keep it running as is. So, I too started looking elsewhere.


Great app, really, but holy cow is it deep and complicated. It can do so much, whenever I spend a significant amount of time using it I start to feel overwhelmed and start questioning how much I really need a single app to do everything when there are individual apps that do things better. Like the text editor, and the PDF markup. Hazel can automatically file things for you, although not based on AI, but it does a good job.

The ability to capture text and web archives is good. And if you really need deep textual analysis of your data, this is the way to go. If not, there are other alternatives.


Did you know Evernote use to be an app that was just one long page? That might have been an early beta or something, I don’t know. Anyway, again, for capturing text and web content, it does a great job, but it’s not really Mac-like, and it’s still a bit of a roach motel for data. Also, I’ve run into weird limits on things when I really start digging in. For me, I’d rather my data stayed on my Mac in a format that I can move around. Except…


My current favorite for managing text, some images, and some captured web content. It doesn’t save web archives, but the Safari plugin will grab the text of the page you are looking at and try to extract the text to Markdown. It does a fair job. Great for storing bits of code and random pieces of information that I know I’ll need later.

Apple Notes

Rich text formatting leaves something to be desired, but syncing is solid and Notes does a good job of being a reliable place to put data. If Apple merged the best of Notes and Bear we’d have a winner. That stupid textured background always annoys me though.

Eagle Filer

A lot like Yojimbo, but it gets updated far more often and keeps data in an open format. Unfortunately it also suffers from the same drawbacks in sync and iOS companion apps. And it also looks dated to my eyes :man_shrugging:t2:.

Everything Else

Let’s not forget crowd favorite Simplenote + NVAlt, which I suppose is still a thing but I’m not sure Brett is ever going to release that updated NVAlt replacement. Then there’s Microsoft’s OneNote, which Circus Ponies blames for killing their Notebook app. If you’re into Microsoft, I guess that’s another way to go. There’s Keep It Together, which I think was renamed just “Together”, and I think abandoned. There’s StickyBrain, which became SOHO Notes, which is now Notelife… I guess? Oh, and let’s not forget the new hotness of Agenda, which combines Notes and a Calendar.

The Finder

Overwhelmed? Me too. That’s why I just went back to the Finder. I feel your pain, I really do. I’ve tried every application, method, and system out there to manage my data, and I still don’t have a perfect system. If Yojimbo was modernized and an iPhone app created, I think I’d have it, but as it is, Bare Bones just doesn’t have the motivation to work on it.

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Great insight, thanks. I don’t really keep web archives, mostly just bookmarks, though maybe I should be doing actual archives, I’ve found more than a couple 404s as I’ve been going back through stuff. I used Pinboard for a while, but I don’t know that that does what I need.

Maybe I just need to clean up my finder, make sure I’m naming PDFs well and use safari bookmark folders for, you know, bookmarking. I may be overcomplicating things.

Apple Notes does bookmarks/links pretty nicely. I might have stolen this from Federico Viticci: I created an Apple Notes file called Interesting Sites to which I save links in Mac/iOS Safari. I save anything interesting I want to to back to - articles, videos, Amazon products, SoundCloud songs, etc.

I used Yojimbo years ago, then Sticky Brain - those were all very Mac-like which is something I miss. I’ve been all in on Evernote-even presenting workshops on EN for educators up here in the Northeast. But the expense and my “shiny new thing” problem led me to try Bear for a bit.

The problem is that, as a very early user of EN, I now have over 35K notes. Importing that many notes into anything would be hard as would going through those notes and figuring out what I can delete.

I have to admit, my workflow in Evernote is really efficient. I use very few notebooks and many tags and in my job I have many Google Docs that are important. Evernote does a great organizing all of those G Docs too.

Putting EN doc links into Things (and previously Omnifocus) is very slick. I was having a tough time with sync - every attachment I threw into EN on the Mac Side wasn’t coming through on iOS. Tech support was very good to me but essentially said that the updater would fix it. It did.

On the “Tools They Use” podcast’, David Pierce of WSJ talked with glee about the app Notion as his Evernote replacement. But it’s an app that does many things that I don’t need such as task and project management.

I very briefly tried Devonthink but I didn’t want to spend the money for it and man, it is complicated and I wasn’t in the place to spend time learning it.

I would certainly consider another option but Evernote if I could cut the cost in half. In the meantime, it does a nice job of meeting my needs.

@bowline So what I’ve settled on for bookmarks for now is Google Bookmarks. It’s pretty similar to Pinboard. I know $11 a year isn’t a lot but I’m really trying to keep the number of subscriptions I have to a minimum. Makes my budgeting easier.

Bookmarks also has an export function so I’m covered if I ever need to get out.

@wcarozza I’ll take a look at Notion. Evernote is like nails on a chalkboard for me. I don 't know what it is about that app, but even the free version drives me nuts. I think it’s like the Adobe apps. They’re so interested in making it cross-platform that it’s not really a Mac app.

I may just need to take some time and work on setting up a filing system in Box or Dropbox or iCloud. Probably iCloud since I’m paying for the extra storage.