According to a group of overclockers who know their shit, PCIe can never outdo PCI in some matters, sound cards for example. In my opinion, PCI-X should have stomped out PCI a long time ago, though. Now, if only someone would actually make a PCI-X card that isn't a ethernnet card.
Yes and no, Vista has no drivers for any ISA device but as it still has a ISA to PCI bridge so as long as you have a Vista compatable driver you can force windows to load the ISAPnP driver, the same way you can get the "unsupported" gameport to work again. Vista is still a pile of shite though.
I'm thinking sound cards, maybe even a decent graphics card. A PCI-X gfx card on my server board would be cool. They probably exist, but 10 prize ranges above me.
I doubt (but can't verify) that any PCI-X vid cards exist as AGP was looked at as the "wonder bus/interface for video" to suceed PCI video, not to mention PCI-X was more or less server-only. IIRC current on-board server mobo video uses either PCI or AGP (or even possibly PCIe if the chipset supports the bus). Fortunately, you could toss a PCI vid card on one of your server's PCI-X slots.
Or any equipment with software you can't recompile. Those are basically (like almost all USB adapters) just FIFO parallel ports. There's no way to adapt buses externally and have them mapped to the actual port addresses, it has to be virtualized, which is usually futile.