Just this morning I've set up a wiki for myself to help with this problem.

As ideas come in, I'll post them to the front page under "free floaters" (working on quicksilver action for that right now), then as they start to form or as I do research, I'll start fleshing out the pages for each idea.

I'm hoping the wiki aspect will also force me to look at how individual ideas might be related. I'm thinking of it conceptually as a mind map that changes with time.

I'm not sure if MediaWiki has the ability to view those relationships at a high level, but if not, I'll write something that does.