If you get that 1-gig card and Vista make sure you get Vista 64-bit so it will recognize all of the ram. The 1-gig is a little overkill and you might be better off getting a 9800GTX, though I don't really remember what your budget is. There's a reason the best single-GPU card only has 512MB of ram; 1 gig isn't necessary or even very useful yet. Not to say you won't see improved performance, but I doubt it would be worth the extra $80.
edit: oh and about PCI Express 2.0. don't worry about it; it is ahead of its time. It doubles the bandwidth between it and the motherboard, but the GPU STILL doesn't fill up the current generation system. It would be nice to know what motherboard you have though.