When I got this motherboard last summer (2004), it was not popular!
That's because it had just
come out. If you'd waited two months it would've been a different story.
I think there are some MBs with both PCI-Express and AGP, but they're extremely few and far between and I certainly wouldn't want to be restricted in that manner -- not to mention that they'll have a significant price premium because it's a specialty item.
And yes, PCI Express has completely taken over now. You can get AGP/PCI boards still, but within a couple years they'll be available in limited quantities (mainly for replacement of boards in corporate environs), and after that it'll be like trying to find a VESA board now. PCI will take a good bit longer to phase out, but since it plays nicely with PCI Express (unlike ISA really) it's a non-issue.
Honestly, if you're not going to go for the 6800GT, just get the 6600GT -- the performance difference between the 6800 and the 6600GT is very small and not worth the additional money.