Somehow we've lost all of the uploaded add-ons off the file server. I'm going to restore one of the semi-daily backups but this does mean that we'll be missing some add-ons and I'll have to deal with those on a per-case basis. I've got someone at the webhost looking into how this happened and I'll also be investigating any sort of rogue script our end too.
I've disabled content-downloading for the moment and things are going to be a bit flaky for a while. Logs indicate that the database went down too, and there were even some problems serving files over apache so whatever happened really screwed us over.