I believe Win9x (and the rest of the DOS-based Windows) has lower input latency than the NT-based ones, largely due to a simpler architecture with shorter codepaths.

Here's a related article: https://news.ycombinator.com/item?id=16001407

But there's a big different qualitative UX interaction latency delta between Win 2k and XP. 2k appeared to have a background thread do all UI stuff while XP and later did not. NT 3.1, 3.5x, and 4.0 (without Active Desktop) all appeared pretty responsive too. ME, XP, Vista... felt really slow.

In terms of apparent responsiveness, Win 3.1x, NT <4, and 2k felt the fastest.