I was mainly playing Unreal Tournament and Baldur's Gate II on my W2KPro machine... UT worked great, BGII alright, but not terribly stable (mind you may for all I know be the same in W98).
However, there have been lots of other games that were for me, way more stable in W98 than in W2K... Starcraft, Starfleet Command 2, Soldier of Fortune, ST Voyager Elite Forces, Janes WWII Fighters.
I just recently experienced the straw that broke the camel's back... re-installed Starcraft (to play lan games with an old laptop we just bought) and although it ran in W2K, it crashed every couple of levels or so... never had that problem in W98. Sooo... although W2K was stable and wonderful, I never really had any problems with W98 stability, dual-booting's a PITA, and so is futzing about with the OS to get games to run... so, I byebye'd W2K yesterday and am now back to W98... for now.