PCIe 1x will soon be replacing the standard PCI card slot, it's basically a slower counterpart of PCIe 16x, but it boasts more bandwidth than standard PCI. Any video card you are looking for will be PCIe 16x, not 1x.
PCIe is a fairly new technology, and due to the fact that AGP is still quite adaquent for today's graphics demanding applications, we haven't yet seen a very large leap from AGP to PCIe. For this reason, there are not very many PCIe manufactured boards at the moment.
As for your original question, the 9800 Pro is the superior card to the x600 which has quite dissapointing performance in my opinion, and the 9800 Pro will be able to handle most games at pretty good settings for a pretty good price.
If you have a bit more money to spend, and I don't think it's a very big price gap between the two, I would scratch the 9800 Pro and get a 6600GT, prefferably on PCIe interface due to it being it's native inferface, but AGP is still fine if that's an issue to you.
Intel C2D E6320 / AMD Athlon X2 3800+
Gigabyte 965P DS3 / DFI nF4 Ultra-D
2GB OCZ Gold PC2-6400 / 2GB OCZ Gold PC4000
eVGA 8800GTS 320MB / eVGA 6800GS 256MB
150GB Raptor / 74GB Raptor
2x500GB / 320GB
OCZ GameXStreme 850w / OCZ StealthXStream 600w