Actually if the machine is capable of running 98se well then you shouldn't be running dos at all. (Ok here it comes for the 357th time) If your have a halfway decent computer than you will actually get better performance on a windows os than on dos. After a certain footprint for windows has been taken care of, dos gives you 0 benefits.
The big benefits DOS does give you, though, are stability (my MAME box never crashed once when running DOS) and a machine that feels more like an arcade machine than a Windows machine in a cabinet. DOS boots far faster as well. Under Windows, Window-isms keep popping up: the mouse pointer appearing during games, the taskbar occasionally popping up, having to "shut down" gracefully (yeah, the power button shuts down gracefully on modern machines, but there's a delay and you can't do it from within MAME), etc. My performance is not noticeably better in Windows, if at all. Windows has been far more of a pain to configure.
I've been very disappointed since converting my cab to Windows; I would go back to DOS in a heartbeat, except that the Act-Labs gun has become by far the most popular part of the cabinet, and that's Windows-only. If I were building a new cab and a lightgun wasn't a requirement, I'd definately use DOS.
But I'll readily admit that I'm in the minority on this issue.
--Chris