I'll post this here as well, since it seems directly relevant.
I had a conflicting personal google account and google apps account. My youtube account was linked with the personal google account. As part of the transition, the personal google account was deleted. What was unknown to me (it wasn't made clear at the time) was that my youtube account would also be deleted.
My youtube account has since been reinstated and linked with my google apps account, and my subscriptions and favorites restored, but my video uploads are still gone. YouTube says they cannot be restored. I think this is ridiculous and find it very hard to believe that YouTube/Google doesn't have backups of everything. I believe the truth is that they don't want to spend the money on employee time to restore these files from archives for individual free users.