To make a long story short: if you’re using Snow Leopard, you have probably noticed that Spotlight search doesn’t show all files on your disk. For example, when you search for a preference file, library or other system files, nothing shows up in results. The good news is that all these files are in fact indexed, they are just excluded from showing up in the results.
To include these (system) files in the results:
1. Invoke a Spotlight search window (not the Spotlight menubar search), default key combo is Cmd-Alt-Space.
2. Click (+) and select “Other…”,
3. Add “System files” from the selection to the menu (checkbox) and then
4. select to include System files in the search:

Then do a search for your preference files, bundles, etc.
How to include system files in Spotlight search by default? I haven’t yet found a setting that overrides the default search scope in Finder, but here’s what you can do: easily create a Smart Folder for an “empty” search that includes also your preferred system files (for instance .plist files) and place it in the sidebar. So now whenever you do a search for system files, just click on the Smart Folder with the extra search criteria before you enter your search term and there are your results (works in Snow Leopard).
Cheers.
(thanks to this article from Tidbits)