I've played with a few but the only one that seems to work properly is ScummVM... The NES and SNES emulators seem to have issues. The NES emulators I've tried haven't be able to do landscape mode... which is stupid. That allows the largest screen and the ability to use the keyboard instead of trying to use ill suited joy stick.
The SNES emulator I tried, did have a landscape mode, but it inexplicabily errors out whenever I try to use it. It's very annoying.... it works on portrait mode, and landscape "left"... but not landscape right... which is what it calls the mode that would have the screen facing the keyboard... so it basically works every way but the one way I need it to. *hate*
Try MorphGear, it plays Nes, SNES, Gameboy, Gameboy Color, GBA, Sega Master System, Sega Game Gear, Sega Genesis, and Turbo Graphics 16. It plays SNES and Genesis really well with sound having the processor over-clocked on your PDA/Phone though.