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.
I wish I could change Kirby's answer from Helpful to Correct, because putting the aperture library in the Spotlight's Privacy list fixed the indexing problem. Now if I could figure out what the NEXT thing crashing my system is...but that's a subject for the USB forum, not Aperture...
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<Edited by Host>
Glad it worked .
Good luck with the USB issue -- I had a USB mouse that caused kernal panics on one machine only. A very willing technician and I spent a week trying to debug it, and then gave up. (Fwiw, that was on -- iirc -- Tiger.)
(PS: I think links such as in your signiture are prohibited by the User Agreement. Our Host edits them out.)
So does anyone know what features you may lose by not having your Aperture Library in the Spotlight index?
Does it limit searching in Aperture?
Think I'll submit a bug with Apple to see if I can get someone to realize that this exists. Wonder if people get the same error with large iPhoto libraries?