I'm in the minority here. I ran a DOS cabinet for a long time... I recently switched to Windows and I regret it. My daughter has gotten addicted to the Act-Labs gun, though, which only works in Windows, so now I have to stay there....
DOS, to me, felt more like a real arcade machine. In Windows, every now and then a mouse pointer seems to appear out of nowhere. Moving the trackball makes it disappear, but it's distracting. I don't like the fuzzy display of the default hardware stretch. I get occassional hangups that I never did in DOS. I seem to get more trackball backspin in Windows than I did in DOS. I have to wait longer for my cabinet to start up now.
Personally, I think it's pointless to run Windows
just to run MAME. (Yes, Howard, that's your cue to rip me a new one.

) The big strength of Windows, in my mind, is being able to run more than just MAME: Windows games like Golden Tee, other emulators like DAPHNE, Visual Pinball, more frontend choices, more jukebox choices, USB controllers, easier networking for updates, etc.
If I were starting on a new cabinet from scratch and wasn't going to put a lightgun in it, I'd definately use DOS. But, again, I'm heavily in the minority, and I was using DOS long before there was a such thing as Windows, so I'm comfortable in that environment. If you are not familiar with the vagaries of DOS such as configuring cards without Plug and Play, memory management, etc., the configuration hassles probably aren't worth it.