As a long time Stickybrain user, the arrival of Yojimbo on the Information Manager front piqued my interest. So I investigated Yojimbo to see if this new app lived up to its legendary name.

Yojimbo wins over Stickybrain:

• Smart Collections (think saved spotlight searches)
  This is very cool (I wish Stickybrain had a feature like this) except I want to be able to query on a LOT of metadata, and not just the 8 different kinds of Smart Collections they have. I also want to be able to combine search terms ("show me recent serial numbers"), and other note attributes ("show me serial numbers I entered last month"). However, at least Yojimbo gives me more power here.
• Drop Dock
  This is just a cool idea - put items into Yojimbo (even into "collections" by just dragging a drawer type thing that pops out onto your desktop. Very Drop Drawers like.
• Print/Import PDFs to Yojimbo
  This is a very cool idea - of course, since neither of these apps are scriptable, I can't "roll my own" workflow where _part_ of it is to import the printed file.
• .mac sync
  Stickybrain has .mac backup/restore, but not SYNC. I can't do this in Stickybrain (unless I am careful and only work on Stickybrain on one computer at a time, which doesn't work at all for those people with a laptop and a desktop.)
• simple installation
  drag and drop the app. Stickybrain requires Installer
• Labels
  A nice feature.

Stickybrain wins over Yojimbo:

• Support for iPod and Palm sync of notes. I want to take my notes on the go with me (sometimes)
• I can associate ("link") a note with another note, or a note with an address. Sometimes this is helpful - it allows me to quickly view related information.
• There's an explicit "back up notes" command. It makes me happy.
• Multiple folder levels.
  In Yojimbo you can't have collections inside of collections. In Stickybrain I have a Writing folder where I have subfolders for all of my current projects. To duplicate this in Yojimbo I would need to use labels (but they'd still be displayed with all of the other notes)
• Services
  Stickybrain has Mac OS X Services that let you save your selection (and submenus that allow you to control which folder you send it to). While "nobody uses services"... well, I do.

The Consumer Loses:

• Scriptability
  None of these apps are scriptable.
• Interface
  Both of these apps _really_ look like Mail. I'm not certain that this is a good interface for random data storage. FWIW, I liked Stickybrain 3's interface better than the Like Mail.app interface SB 4 has.
• No OPML support
  I'd like to be able to import a series of notes from an OPML file
• Find
  In the days of Spotlight, multiple search terms, and metadata, both of these apps' built in search features feel lacking in this department. Yes, Spotlight indexes both application's notes, but doing a Find inside the app itself logically narrows down the field of information - but it just feels like my searches are limited by one search attribute. Yojimbo lets me search on some metadata (more than Stickybrain) but it still feels really limited.
• Bad text editing
  I expected better from BareBones - they have this great text engine in BBEdit, many times better than what is in Cocoa... but they are (apparently) using Cocoa's. I can't Hard Wrap my text, there's no philip bar, no prefix/suffix, no grep find. I know Yojimbo isn't a text editor... but come on guys. (Stickybrain doesn't have any powerful editing capabilities beyond Cocoa's text control either, but I expected more from the makers of (some say) one of the best text editors on the planet.)

Answer: While I really like Yojimbo's .Mac sync services, I think it feels very "lite" compared to what Stickybrain can do for me. The interface feels fast compared to Stickybrain, and it has potential, but I'm waiting for Yojimbo 2.0: Now With More Ninja.