Don't forget that My Documents is on c: by default.
Hmm, that's true. That should definitely be fixed. I don't even think we map the home directory in wineprefixcreate by default, do we? I think Marcus' patch adds that.
Also, reinstalling all apps just because you upgraded Wine seems a bit overkill, no?
Well, yeah, but over time I think it becomes necessary as the contents of the initial registry/config file change etc ... it's hard to know exactly what you need to do so reinstalling is the easiest way.
It sucks, I agree.