The most common issue is a logger database problem. Usually the logger is corrupt or just not functioning, and the admin never attends to it (or just doesn't care). The upgrade script tries to start it, and access it, but fails resulting in at least 3 of the problems I've seen.
We could do more to prevent this condition, so last night we had a discussion about it, and in 5.0.13 we will give the user an option to check the logger db before upgrading. We already do that for the mailbox mysql db.
A thing to remember is that most people who never have an issue with an upgrade, never post. People only usually only post if they have an issue.
The good news is that the Zimbra community support is by far the very best of anyone. We have some just fantastic moderators and contributors who all stand ready to help should something bad happen.
john