Why wouldn't you use xp?... It has nearly the exact same kernel as 200 but the added bonus of having 2d hardware acceleration on the desktop, much better multimedia handleing (very good for daphne) and better gaming support.
Honestly I would reccomend 98 over 2000. 2000 was the nt version of the lame-o os threw to the public before xp was ready. It's kind of like the nt version of windows Me! (Well not nearly that bad but you get the idea.) The main difference between 2000 and xp is xp was designed for the end user and 2000 was designed for the office. In other words xp is better for gaming even though it sometimes requires slightly more resources than 2000.
I ran 2000 at work and xp at home. The two machines had similar resources and I would play the same games and run the same emulators on each (yeah I know, I shouldn't be doing that at work but oh well

) For really really high end games the 2000 box would beat out the xp box by the sheer amount of free resources. However, on mid to low level games the xp machine would always out perform the 2000 one. The xp machine would get the same (or slightly higher) framerate as the 200 box, but things would be rendered smoother and there were less graphical glitches. (tearing, ect) Also multimedia was a no contest... videos in 2000 were rather cumbersome (for lack of a better description) on 2000 as they are in win 9x os'es. The xp machine was smooth as slik however.
Just my opinion, you'll figure it out on your own eventually.

Honestly though, 2000 will be much more stable than 98 but at the cost of having far worse gaming support. Xp is the best of both worlds at the minimal cost of requiring more system resources. Of course if your building a mame cab then you can turn off the themes and that cuts the required resources down by about 40%