Mediawiki for big stuff, plain old Stickies for little stuff, paper away from the desk (it's harder to break). I had tried StickyBrain a few years ago, but (at least at the time) it was buggy and had a nasty tendency to corrupt its own database.
One last question... does it bother you that it appears to be one person and not a whole open source team at Wikinotes? that's my first impression anyway.
If mac could just get Stickies to have some of the cool linking functions... or even host an open source community site for developers and hackers to do their open source thang, then I'd be really rapt.