I've been testing Win2k Pro as well, and I've found that a the newer games you mentioned that don't run have problems due to Directx 7, which is in Win2k.
Not that EF2 or WF have had any time from me since getting the CM beta demo! DOS games - oh well, TOP2 and PITS have been burned to CD and they run fine in NT4. THat's all I care about with DOS.
I'm running Win98 too, and to save headaches install Win2k from Win98 and make sure it goes on its own partition. That way, if you want to get rid of a Win2k install, just make a boot disk from Win98 (DOS 7), copy over sys.com. boot from the disk and run sys c: