Since (apparently) later versions of 10.5, Spotlight has a file called VolumeConfig.plist which you can edit to index only certain directories. For example, I wanted to index only my Mail folder and my Documents folder because those don't usually have radical changes, and they're the only places I ever need search (especially Mail). To accomplish this, I first disabled Spotlight indexing on my hard disk:
sudo mdutil -i off /
Then, with root permissions, I opened /.Spotlight-V100/Store-V1/VolumeConfig.plist and edited it. I changed partialPath to Users/myusername/Library/Mail (note the lack of a leading slash), and policySearch to 3.
sudo launchctl stop com.apple.metadata.mds
Now that you've set up the new indexes, you should be able to control them using mdutil:
mdutil -sv ~/Library/Mail
Use caution however, as you may undo your work if you run mdutil -i on /.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20090914124459567