Spotlight kept indexing my home folder (protected by File Vault) never stopped trying to index it, and was therefore unusable. To find out what Spotlight was up to, I ran this command in the Terminal:
lsof | grep mdimport | grep /Users/`whoami`
I then saw that it was choking on old corrupted files, which I removed -- or if it chokes on a particular directory, you can add this directory to the Privacy tab of the Spotlight preferences pane. Hope this helps

