This covers 98, 98SE and ME because they're pretty much the same Windows with no notable differences game-wise (and there are practically no games that support ME but not either of the 98 variants).

For emulation/virtual machine purposes, you should prefer 98SE as it is the most compatible and likely the most stable one.

Win9x supported only single CPU, so you may have to take this into account when running games made for it on modern operating systems and hardware. For example multithreaded games might get into race conditions, crashes, hangs, etc.on systems with multiple CPUs, cores, or such.