WHY? WHY? WHY DO PEOPLE ... create a separate apps partition?
If you have to blow away one of the PS partitions, you will still have to reinstall the apps to restore the registry entries.
And, as far as *I* am concerned, you do NOT need to run the same apps from both OSes. Win2K is likely the OS where you do all of your real work. If you only want Win9x for games, why bother installing all of your other apps in Win9x when you won't even use them there?
IF ANYTHING, create a separate partition to keep your personal files (AKA "My Documents").
As far as I am concerned, dual/mutli-booting is NOT intended for running all of the same apps everywhere. Use each OS for its strength. I would say that XP/2K are there for stability, so you do your real-world stuff there. Anything that doesn't work, revert to Win9x/ME/NT4/etc.
Am I way off base?
-SUO, runs 6 OSes on his machine, yet only one install of, say, Office ... for only one OS