On my 17" CRT monitor I prefer to use 1280x960, but due to a bug ( emulator's fault or video card's I am not too sure ) I stick with my desktop default setting, which is 1024x768. This way the system doesn't hang up when switching between full screen/windowed.I also use 60 herz refresh rate as I noticed that some games that are supposed to run on a television are kind of smoother when played at the same refresh rate they where ment for.
For more details check my older post " games framerate smoother then on real hardware ".
Armando