If you have a 3rd party app that isn't behaving well with Spotlight, you could try surfing to ~/Library/Caches/Metadata. This is where apps, especially database-driven ones that want to be indexed by Spotlight, place cache data in order to make it into search results. For me, simply quitting Yojimbo, tossing out the Yojimbo folder sitting inside that Metadata folder and restarting Yojimbo forced Spotlight to get to work. The little magnifying glass began flowing on and off, and my Yojimbo items were soon appearing in my Spotlight search results just as they should.
Now I don't know if this is the end-all solution to Spotlight indexing issues like this. I only know it worked for me, and judging from the emails that occasionally bounce over the Yojimbo mailing list, I'm not the only one who's ever tangled with Spotlight's indexing quirks. I hope this tip can help you unravel any Spotlight searching issues of your own.