Well, consider what you are going to be playing. If you are going to want to play the Killer Instincts or some of the other "newer" games, go for a WinOS. If you just want Donkey Kong, ETC. I'd say go for DOS.
With an Athalon 2100+, Killer Instinct plays like crap. It is marvelous under Windows (Iattribute the Direct Draw drivers).
So, I will try to explain the pros and cons:
DOS PROS
Cleaner images
Faster startup
DOS CONS
Fewer emulators available
Newer games run slower
WINDOWS PROS
Networking is simple (easily update your ROMs and emulators)
Easily configurable to run most emus through MAMEWah
WINDOWS CONS
Image looks worse, even with stretching off (direct draw).
Can crash to desktop
Popular front ends can't do vertical configurations (yet).
Incomplete, I know, but I think this might help your decision.