After comparing many programs for my regular note-taking, I keep returning to Yojimbo. The tagging system and spotlight support are enough for me to find my misc notes. Syncing via .Mac has a nice wrinkle in that it will merge changes to individual files, so if you update a file on one computer, and another file on the other computer, when you sync them both changes are reflected on both machines. Still, while the tagging approach can be fast, creating more complex relationships is difficult, if not impossible. In the end, Yojimbo is not ideal, and I'm still planning on trying alternatives, but this is what I have.
What's worse, I'm kind of painted into a corner because BareBones has decided, in their wisdom, to provide no way at all to export your items except one at a time. There's also no way to export for backup, unless you want to manually back up the Yojimbo Application Support folder in your user Library.