Those DOS freaks! Can;t get rid of that OS:) Missing out on some awesome games that could be in your cabinet, like big race pinball, golden tee golf pc, and nfl blitz.
Hahahahaha! DOS keeps it a retro experience for me.

There are benefits to both the DOS and Windows OS's, so it's really what's important to you that leads to the decision. Definitely more software available for the windows user. But like Chris, I'm not familiar with much of it. My non-emulation gaming consists of Wolfenstein 3D, Jumpman, and the commander keen series!

The only thing that I feel I'm really missing out on is Peters Emulaxian frontend. I drool over pictures and descriptions and his website, but won't download it for fear of having to convert my machine to windows!

The big DOS bonus, and I can't stress this more (even though it has been mentioned) is the ability to just shut the thing off in the middle of any game. 'Shut down' the arcade cabinet?!?

Other perks, no need to ever use the mouse (keep it as far away from a computer experience, I work w/ em 8 hours a day), Ease of use/setup (if you are already familiar with DOS). No need to disable a billion things from windows, delete icons, camoflauge the fact you are running windows, etc. Speed in general (no windows overhead), and a daaaaamn quick boot speed.
In the early mame cab days, dos was the only answer (unless you were command prompt-phobic), but these days they both merit. I just hope they keep compiling a DOS mame, or soon DOS won't make any sense at all.
Right now, though, it really boils down to a speed vs. software availability issue.