Spotlight indexes at the file level, so a file containing a complicated data structure may need to be split into a set of files for Spotlight to index it in a useful way.
Can you use MacFUSE to achieve this more dynamically?
Will Spotlight index a MacFUSE volume?
Can MacFUSE handle the necessary per-file metadata?
Can a MacFUSE process notify Spotlight when attributes of a file change?
I've been testing with this myself.
I found this on the MacFuse Wiki: (http://code.google.com/p/macfuse/wiki/OPTIONS) if you wish to use Spotlight on a MacFUSE volume, you'll need to use allow_other.
I've discovered that it also works with allow_root.
However, I had to enable indexing myself by using mdutil -i on /Volume (as codelogic already mentioned)
So, if it does not work, try allow_root or allow_other
More testing: Allow_root does not work. it can index once, but it doesn't seem to index newly created files in subfolders. When changing to allow_other, it seems spotlight CAN detect the new changes, and index the new files. ==> allow_other is a requirement