I've been messing around with gambatte also, as you can see I posted a .deb in here, it's not gtk/hildonized at all, but has some improvements. However, on a whim, I compiled gnuboy, and I have to say it works a lot better than gambatte. Less CPU usage and runs better. It also based on SDL, and works much the same as gambatte. I might have a .deb similar to my other one out shortly with gnuboy.
However at the moment I am stuck trying to get the YUV overlay to work decently. It is terribly slow. I don't suppose you got anywhere with the YUV mode of gambatte? They seem to work pretty much the same, and both give absolutely terrible performance, even though the N800 is supposed to have hardware YUV scaling. I have been poring over the quetoo and ur-quan masters source looking for differences with their YUV overlay modes, but haven't had any luck speeding it up.