The file fb.db has to be there. It's part of Leopard. Are you sure you're looking in the correct location? It's in your user account at Home > Library > Application Support > Font Book.
This telling, though.
There is no fb.db file. And starting in Safe Mode doesn't change anything. I didn't even lose my collections.
A couple of things here. Is there more than one account on this Mac? Whichever one you login to from during a Safe Mode boot is the one which will be cleaned out. So if you logged into a different account in Safe Mode, then indeed nothing will change in your account when you boot again normally.
If there is only one account and nothing changed after a Safe Mode boot, then I would Repair Permissions on the drive and try again. If that doesn't work (and probably won't), then I think a reinstall of the OS is in order.
I've flirted with FontAgentPro but it only recognised half my fonts...
That again could either be a symptom of an OS that needs to be reinstalled, or, because FAP stores all activated fonts in it's own location, it could just be that there are multiple font conflicts between the stored fonts and those same fonts still in the various Fonts folders.