If you're not satisfied with Spotlight's performance, or lack of customization, you should check out Meta, from Big Robot Software.  It's a version 2 release and it looks pretty strong in features.

With Meta (Spotlight's Bigger Brother, as they have tagged it), you can easily limit the directories that get searched, on the fly!  No more checking and un checking directories in the Spotlight Prefs.  You can also add and append Spotlight Comments to files, using Meta, so that you can apply your own method of custom metadata tags for sorting and searching with better results.  Creating custom query folders is as simple as a single click.  And you can even combine simple or complex query strings for more specific results, as suits your needs/style.

There's a 15 day free trial on Meta.  If Spotlight's lacking in the areas you're looking for, give Meta a try.