Voted win98, but like a few others said, really depends what you want to run.
For me, it would be win98 because I want to include dual/multiple trackballs & lightguns. My desktop system currently runs winME, which also does this, so my second choice would be winME. Not the best OSs, but if you clean up win98/winME, it'll be okay if the cab isn't on 24 hours a day.
If you don't want to play 2 player marble madness and the like, and your system isn't "ghetto", winXP is more stable and should do fine. Linux & advanceMame is another stable option, especially if you're doing an arcade monitor, but you need to know *nix to set it up, and windows has more front ends. Either this OSs should be able to run 24/7.
If you have an old computer (500mhz and slower), don't need to play the cpu intense games, and don't need USB, go with dos.
That's my 2 cents.