I will keep this short: Applications that don't handle intermittent network connectivity well. (That would be pretty much all of them, in my experience.) The software that bites me with this problem almost every day are Evolution (specifically evolution-exchange-storage) and Gaim. I'm sure there are others though.
Right, that's it! There are no more things about GNOME that Suck (in my not-so-humble opinion). Remember, this was about GNOME as a desktop environment, from a user's point of view. Your opinions may (and almost certainly do) differ from mine, so if you feel strongly about these issues, blog about them!