BareBones software new product looks very similar to DevonThink:
barebones.com/products/yojimbo/index.shtml
I guess the competition is good although I doubt that the initial version is any match for DevonThink.
The most (and only?) interesting feature of Yojimbo is probably its interface but DT Pro v1.1 will simplify/improve a few things too (just the first steps towards v2 
)
Are you serious? I don’t think you’re being honest if the only good thing you see in Yojimbo is the interface. It’s no real competition for DTPro, sure, but there’s more virtue in Bare Bones’ entry than just eye candy.
For example (and this is based on about five minutes playing with the Yojimbo demo):
Flagged items
Recent Items
Item-by-item encryption
But that’s just surface stuff. You could add that as features to DTPro as a dot release. I think a more serious competitor is Hog Bay’s Mori. I think it works along side DTPro, but there’s also some good lessons to be learned there.
A professional interface
Smart folders
The smart folders are where there’s some real hot-dang-wow going on. You could really add some nice power and usability to DEVONthink by adding smart folders (or saved searches, which is essentially the same thing). About once a month I wonder if smart folders is already in DTPro and I’ve just missed it. Nope. I sure wish it was.
Smart folders. Yes, smart folders.
What do you mean by smart folders? DTpro has smart groups, this is the same functionnality. (or do I miss something?)
I agree that Yojimbo is a nice application, but I see it closer to (an probably better than) macjournal or mori. Although the interface of DTPro still deserves some improvement, DTPro is quite far ahead from these applications (that’s my opinion as a user of DTPro, for professional purposes, and daily work.)
Alb
No, you don’t miss anything; I do. I just this minute found the “Smart Groups” script – which is why I probably didn’t find it sooner, and think it’s still only 80% there: it’s just a script.
So I stand corrected, and I’m happy about it. Smart Groups exist.
However, I would still like to be able to (search and) create smart groups for file types, creation and modification dates, etc. Right now, I can use a script to create a (non-visually distinguished) word-based smart group. It’s a great start. But just a start. Once it has all the functionality, and it appears under the Data menu, then I’ll know it’s really there.
I agree that DTPro is the best out there. And I, too, use it daily for my work. But I’d rather have a paranoid group at DEVON technologies, always concerned that someone was about to eat their lunch. Being the best does not always mean winning – and I want to see DEVONthink survive and thrive for the years (and years and years) to come. That means looking at any competition and deciding if there’s anything that they do better. And then incorporate those improvements back into DT.
–jw
Well, at least I am paranoid And v2 will introduce real smart groups (among many other things), the current ones are (more or less) just a demonstration of the scripting capabilities of DT Pro.
Beautiful! Give yourself a raise, and then get back to work. We want v2 now!
–jw
I agree with a lot of the posts here. I tried Yojimbo - it’s neat but far more limited and inflexible than DP. When DP latches properly into the file system with Version 2 it should be an unquestionably superior product
I would add to all this that Yojimbo is far more “accessible” to a new user than DT ! I come from a very old archive system (Marco Polo - under OS9) and am looking for something to replace this unvaluable tool. I came across DT, Yojimbo and others … Up to now Yojimbo seems very easy, with nice features “to the point”. On the other hand, DT is hard to really understand “what it is about”, how it really works, what it does with your files, etc. Furthermore, I posted a “request” on this forum a few days ago with these “questions” and no one answered my doubts … (removed the post in the meantime). I also understand that many things are still “under development” for an upcoming version which will probably be closer to something I can “realize”. My message is perhaps slightly negative but I want to see it in the direction of “this product is probably worthy but not affordable at first sight at all”. Progress could probably be made in this direction because I can’t “loose my time” in trying to use or test a software that I’m not even able to get what it is really doing 
Maybe I’m too stupid for this very “intellectual” software ?
The next release should simplify this a lot by removing all those copy/don’t copy options (and several others) and by combining “File > Index” and “File > Link To”.
Although DT Pro is a great document manager and can handle larger databases than the other applications mentioned above, IMHO DT Pro’s artificial intelligence features set it apart from others.
My main database covers broad areas of environmental science and technology literature. Whether I’m researching a particular environmental pollutant, a technology for remediating hazardous waste sites or comparisons of environmental laws and regulations in different countries the See Also button makes DT Pro a real research assistant. DT Pro suggests other content that may be related to the document being viewed. Although it’s the responsibility of the user to decide whether or not the suggestions are really relevant (after all, DT Pro really isn’t trained in chemistry or toxicology or engineering or policy analysis) See Also often prompts me to connections between data or concepts that are new to me, and that can be really exciting.
Last year, Steven B. Johnson wrote an article in the New York Times (January 30, 2005, Tools for Thought http://www.nytimes.com/2005/01/30/books/review/30JOHNSON.html?ex=1139720400&en=1efff7174b60c139&ei=5070 describing how he used DEVONthink to support his writing projects. He used DEVONthink’s ability to suggest related items in his database.
Here’s an excerpt from Johnson’s article:
" For the past three years, I’ve been using tools comparable to the new ones hitting the market, so I have extensive firsthand experience with the way the software changes the creative process. (I have used a custom-designed application, created by the programmer Maciej Ceglowski at the National Institute for Technology and Liberal Education, and now use an off-the-shelf program called DEVONthink.) The raw material the software relies on is an archive of my writings and notes, plus a few thousand choice quotes from books I have read over the past decade: an archive, in other words, of all my old ideas, and the ideas that have influenced me.
Having all this information available at my fingerprints does more than help me find my notes faster. Yes, when I’m trying to track down an article I wrote many years ago, it’s now much easier to retrieve. But the qualitative change lies elsewhere: in finding documents I’ve forgotten about altogether, documents that I didn’t know I was looking for.
What does this mean in practice? Consider how I used the tool in writing my last book, which revolved around the latest developments in brain science. I would write a paragraph that addressed the human brain’s remarkable facility for interpreting facial expressions. I’d then plug that paragraph into the software, and ask it to find other, similar passages in my archive. Instantly, a list of quotes would be returned: some on the neural architecture that triggers facial expressions, others on the evolutionary history of the smile, still others that dealt with the expressiveness of our near relatives, the chimpanzees. Invariably, one or two of these would trigger a new association in my head – I’d forgotten about the chimpanzee connection – and I’d select that quote, and ask the software to find a new batch of documents similar to it. Before long a larger idea had taken shape in my head, built out of the trail of associations the machine had assembled for me.
Compare that to the traditional way of exploring your files, where the computer is like a dutiful, but dumb, butler: ‘‘Find me that document about the chimpanzees!’’ That’s searching. The other feels different, so different that we don’t quite have a verb for it: it’s riffing, or brainstorming, or exploring. There are false starts and red herrings, to be sure, but there are just as many happy accidents and unexpected discoveries. Indeed, the fuzziness of the results is part of what makes the software so powerful.
These tools are smart enough to get around the classic search engine failing of excessive specificity: searching for ‘‘dog’’ and missing all the articles that have only ‘‘canine’’ in them. Modern indexing software learns associations between individual words, by tracking the frequency with which words appear near each other. This can create almost lyrical connections between ideas. I’m now working on a project that involves the history of the London sewers. The other day I ran a search that included the word ‘‘sewage’’ several times. Because the software knows the word ‘‘waste’’ is often used alongside ‘‘sewage’’ it directed me to a quote that explained the way bones evolved in vertebrate bodies: by repurposing the calcium waste products created by the metabolism of cells.
That might seem like an errant result, but it sent me off on a long and fruitful tangent into the way complex systems – whether cities or bodies – find productive uses for the waste they create. It’s still early, but I may well get an entire chapter out of that little spark of an idea.
Now, strictly speaking, who is responsible for that initial idea? Was it me or the software? It sounds like a facetious question, but I mean it seriously. Obviously, the computer wasn’t conscious of the idea taking shape, and I supplied the conceptual glue that linked the London sewers to cell metabolism. But I’m not at all confident I would have made the initial connection without the help of the software. The idea was a true collaboration, two very different kinds of intelligence playing off each other, one carbon-based, the other silicon."
Johnson’s database contains many relatively short items, and he concluded that the See Also feature works best with such relatively short items.
But many of my reference items are quite long, some running to hundreds of pages. I don’t want to break up all of those documents into short segments to take maximum advantage of the See Also feature.
The next release of DT Pro (I’m working now with a beta version) will improve the operation of the See Selected Text contextual menu option, which becomes available when one opens a document in DT Pro and selects text. If I select an appropriate section of a large document, it emulates Johnson’s “granularity” condition. Suppose I have a PDF document that’s a manual for analysis of environmental pollutants, but I’m only interested in techniques for analyzing mercury in fish samples. Now I can select just that section of the manual and use the Selected Text operation to find other documents in my reference collection that deal with mercury in fish samples. Yes, I get useful suggestions from DT Pro that are much more to the point than if I had used the See Also operation.
That’s why I call DT Pro a research assistant, not just a document manager. 
Thanks, Bill, for your typically thoughtful reply. However, I’m still curious about Yojimbo. I don’t really need many of the AI functions of DevonThink, which is why I use DevonNote instead. So I’m curious how Yojimbo stacks up against DevonNote. Certainly I’ve encountered my share of Devon confusions (as noted by many forum contributors) but am pretty comfortable with it now. Still, I’d be interested to know what features Yojimbo has that DN lacks (and vice versa), and also which ones DN’s developers are considering adding to upcoming revisions of DevonNote.
I haven’t played with Yojimbo, but others have.
But DEVONnote also has some of the AI features I was talking about. Try the “See Also” button in DEVONnote – it’s there!
I own DEVONthink, NoteBook and Yojimbo and to me they fill different needs. Yojimbo, is the lightweight notekeeper that’s always accessible, NoteBook is the place where to organize stuff to do, write notes etc. DEVONthink is the place to store research info and more “heavyweight” stuff.
I have been using DEVONthink off and on since 2003 (Personal edtion now but thinking of going Pro.) I have downloaded Yojimbo and most other note-and-clipping applications for the mac. IMO none is as good as DT for my purposes. And none comes close to DT’s search features (I love See Also and the ability to option-click on a word in one DT item and get a list of similar items.)
Some Yojimbo-only features: encrypted notes for passwords, out-of-the-box structure with pretty icons (you can add your own icons to DT’s group folders, btw), a dock-like application for draging-and-dropping clippings.
I may be the only person who doesn’t like this last feature: it’s a second application that runs in a addition to the main Yojimbo application; I don’t like having lots of little applications running in the background (not a fan of widgets either.) I prefer to drag to the dock or the Groups panel. Also, I don’t believe Yojimbo will let you create subdirectories (sub-groups), I can’t double-check that because my demo ran out. In about 10 minutes of use I exceeded Yojimbo’s useful features and got bored with the pretty icons .
My only complaints with DT are 1) the confusion over having too many ways of accomplishing the same thing (which can also be seen as a plus), 2) complicted preference settings, and the confusing storage schemes (database, linked files, stored files.) Recently, I gave up my Palm and added my PIM record-keeping to DT; now I keep DT open in a corner of the screen. As far as I can tell, most of these issues will be addressed in coming updates.
The next releases (DT Pro 1.1 and DT 1.9.7) should improve most of these issues. (especially no. 2)
From time to time, users have suggested the possibility of encryption for certain documents (as is done in Yojimbo, for example).
That creates a special problem for DEVONnote/DEVONthink Personal/DEVONthink Pro, because of the contextual recognition features that are typically lacking in applications such as Yojimbo. If a an encrypted document is “open”, the contextual recognition features work. If it is encrypted, they don’t work (at least in the same way.)
So far, we have recommended to users that if a database contains sensitive information, the best approach is probably to encrypt the entire database, e.g., in an encrypted disk image. There’s also a simple password protection scheme available to users (File > Database Properties) that password-secures the entire database, but which is not as secure as running the database on an encrypted disk image. In either case, please don’t forget your password.
One could also use Apple’s File Vault protection. Personally, I don’t do that, because it would make data recovery difficult if not impossible should anything go wrong.
I’m toying a bit with INtex Daily vX 1.2, a journal and note taking piece of software. it’s a FileMaker app so it won’t be to everyone’s taste but my first impression is: not bad.
Check out their website here.
One thing INtex Daily vX and Devonthink have in common: they both come from Germany.
I also tried lots of note taking/journal software: MacJournal ($34,95), Dossier ($19) and Journler (free!) come close to INtex Daily - and i would prefer them, cause they are not FileMaker apps.
Also i would say, it’s not so much/not only a question of the quality of these applications but first of all, if they meet your needs/style of work.
For my own needs the triumvirate is clearly OmniOutliner, Hogbays Mori and DEVONthink Pro.
Speeking of competition one should quote these lines from the Hog Bay Software website:
Thats fair towards costumers and competitors 
On keeping notes on a daily basis - i have a group “journal” in my main DEVONthink database and i a add rtf-documents with the date as title (should write an applescript to do this).
For outlining, I have very simple needs. I don’t need a full-blown outliner like TAO — a good piece of software but the developer doesn’t do justice to his work due to a stupid versioning scheme — or OmniOutliner. As for INtex Daily, it’s unuseable for me: no access to the Services menu But I’ll keep an eye on it because it has some nifty features. Journler and MacJournal are very good but they have a podcast creation feature that I don’t need at all. Dossier is a piece of software I never managed to get into.
StickyBrain could be excellent with a better stability.