You could then just run ctags from inside Vim to give you a full index.
But, I hate it. I would love to switch to something else. Maybe just plain text notes in a directory stucture indeed.
I started out organizing my ideas in a single hierarchically organized text file (I call it ideas.org because I use org-mode) based on the categories of my ideas, and as each category grows, I place it into its own text file, replacing its former place in my ideas.org file with a link to the new file (this is where it sure would be nice to have Ted Nelson-style transclusion). As each category grows subcategories, I place those into their own files too.
Ctrl-P let's me search via file names, Find all within the project directory lets me flip through the entirety of my notes. Works fantastically. I'm sure with CTags or some such plugin you could get really serious with this, but this suits my needs perfectly fine and is simplistic yet powerful.
Keepnote is worth checking out, if you're on Windows or Linux, but it runs like crap on OS X.