I found that Spotlight was often not finding files when searching for words within the file (file names seemed to be OK).
I found various threads suggesting that it may be a problem with File Permissions. I use Dropbox and was concerned it may have messed up permissions after a relinking a while ago.
I tried to reset permissions from within Dropbox (under Settings), but no help.
Finally I found this EXCELLENT TIP to reset permissions from within the Repair Utility (in Mountain Lion), Not the Disk Utility, which I had not been aware of: https://discussions.apple.com/message/20421138#20421138
It took a little while and then Spotlight re-indexed all my files. SO FAR it seems to be working well.