Your best bet is Windows 2000 or XP. 2000 is a little bit better, although from what I hear XP loads up a little faster. The biggest advantage to Windows over DOS is that you WILL get much better Mame performance. As much as I hate Windows and hate using WIndows in my cabinet, it DOES give better performance than DOS. Oh well. I just have my cabinet boot up and then it starts Game Launcher (the best FE for a cabinet). You can use any emulator with Game Launcher too. I'm running Mame, VirtualNES, ZSNES, Gens, Magic Engine, Daphne, etc... It works beautifully.
Whatever you do, don't run Windows 98 or ME. They suck compared to 2000 or XP for what you need it for. If you have ever used 98 before, you will notice that if the computer it used and not reset for too long (like a day) then the OS will start to slow down. This will not happen with 2000 or XP because the architecture is different and the NT kernel doesn't want to cache every single little thing like 98/ME.