I'm using mame.exe (windows version). I never change color depth or screen size and always use HWStretching.
Everything runs great with that. I'm running with a Geforce2mx so the HWStreatching is great.
btw, it does handle 640x480, 320x200 and 320x240 so you do have some of the resolutions that are native. But they don't make any difference in my mind when playing at 320x200 or 640x480 hwstretchin... so I stopped messing with the settings.