I've heard that RockApp also had a BackUp utility that is supposed to work nicely, but I have no first hand experience with it.
I also once SSH'd some files/preferences out and restored them when I updated - but I could not tell you which ones they are (I don't remember).
Either way, I'm still on 3.0, because I don't think it's worth the hassle of updating quite yet. Unless you're having problems, it's probably easier to just stay put.