From Kelley Computing:
By default, Apple's new "Spotlight" feature in Mac OS X 10.4 has been a saving grace for local searches. One limitation that ails this software is the fact that it will not index hidden directories; some that Apple deem off limits. SpotlightIndexer will allow the user to easily index folders that may not currently be searched by Spotlight. This software does not modify the way that Spotlight runs, or alter it in any way. The program simply uses the same process that Spotlight does to import files and folder contents into its index. SpotlightIndexer acts as a front-end to the command line utility mdimport.