I've just installed the Firefox 6.0 Beta as FF5 was kind enough to remind me of its availability. Scripts like BOB and Saved Searches seem to be working just fine at first glance, but right now I can't view/enable/disable my scripts through Tools -> Add-ons -> User Scripts. It simply doesn't show any entries, so for the time being I wouldn't recommend updating to FF6.
I will check if reinstalling GM 0.9.6 resolves this issue.