I've been using Yojimbo for a couple of months now and it's really changed the way I work and take notes. I was for years (and too some degree still am) a diehard Moleskine user and have a stack of completed journals on my bookshelf to prove it. The one problem I always had though was searching for notes and hence my new love affair with Yojimbo.
The Yojimbo Talk mailing list has recently been flooded with many new feature requests, most pertaining to nested/smart/… folders. The Bare Bones team has made it pretty clear they are focused on a GTD approach of tag-and-search, a decision with which I whole-heartedly agree. I chose Yojimbo because it didn't have too many features.
There is however a bug with search that affects my workflow. I'm still using a holdover from my Moleskine days whereby I prefix certain words with "@" such as @talk, @todo or @followup. Unfortunately it looks like Yojimbo doesn't consistently handle "@" when embedded in the text of the note. It appears searching escapes the "@" from the query string which results in some erroneous entries being found. Text highlighting on the other hand doesn't escape the "@" so the query string isn't highlighted in the resulting note. I think the bug is with search. I suppose I could make these tags but either way the search functionality has a bug.