I tried searching the interwebs and all I could come up with was several recommendations that I try removing and re-adding folders from Spotlight. None of that seemed to work for me.
In the end I decided to do a full reindex of Spotlight, which can take quite a while. In the case of my MacBook with a 320G drive (197G in use) it takes nearly an hour. The machine is perfectly useable during that time, except that you can't use Spotlight until it's complete.
If you need to do the reindex simple open a terminal window and plug in the following command:
sudo mdutil -E /
Once that kicks off (you'll need the administrator's password) you can close the terminal window and continue working, though the CPU on my MacBook was pretty busy for a while.
When it finally did come back Spotlight could again find everything. If you get the situation where Spotlight can't find some files try these suggestions first. If that fails then ensuring you have all of your Spotlight folders properly selected (Preferences / Spotlight) and then performing the reindex above will likely fix the problem.
You can also see the progress of the indexing by placing your mouse over the Spotlight icon to get a reading of the percent complete on the indexing. Thanks to MacWorld for highlighting that little gem.