Having a brief look around it seems AGP will still be supported for the time being at least but yes as more people move to PCI-E and it is improved then AGP will fade away at least thats what I think anyway
...is to look on motherboard manufacturers websites, and have a look at their new line up of motherboards.
Keep an eye on it for a while. I think most of them now are only making PCI-E boards, BTX is the new standard too.
Graphics card manufacturers will continue to pour off AGP cards as there are still people who currently have AGP boards installed. I've just bought a new 6800GT AGPx8 card.
However, if i was to build a new system i'd buy a PCI-E board. At the end of the day, you have to sit down and think about what you're going to use the PC for, how much you have to spend, whether you'll be wanting to upgrade within a few years or buy a new system if at all.
If you're a speed freak, which you don't seem to be, then you'd just buy all the latest clobber you could afford.
In your case you're building a new PC, so i'd suggest moving to PCI-E. In theory, you'll be able to upgrade componentry for at least a year or two.
I'd look towards buying a BTX PCI-E system. Just keep an eye on the coming soon sections too.