Do you need Spotlight to index your Library? I'd put it in Spotlight's "Privacy" list (i.e.: "ignore these"), then reboot and then repair your Library (using the usual trouble-shooting tools) and then reboot again.
Once that settles down, you can add your Library back, but you should set it up so that Spotlight can run uninterrupted at least overnight. The initial indexing is the problem (or was for me, under Snow Leopard). Once it was finished I had no further problems.