The biggest annoyance for me has to be the fact that the gnome panel constantly seems to get confused on the order in which icons and gadgets should appear. I'll spend 30 minutes getting the notification area, icons, menus, etc arranged just as I like them, and then notice the next time I login that they're rearranged. And God help you if you ever resize the panel, even temporarily, because they get completely screwed if that happens. It's very frustrating, and is a problem that's existed since the gnome panel was invented (yes, I've been using it that long). Even more frustrating is that once they're screwed up, they seem to tend to lock in place to the extent that fixing them back the way you like becomes a real exercise.