Personal preference is AMD with PCI-E...
In your case I'd go for AMD with AGP coz you'll still get very decent AGP cards that'll last you long and give nice gaming...but Bjorns right it depends what you wanna use it for
jeez thats a tough one.
if you go the amd/agp remember the 7800gs will probly be the last high end card for agp.
So i would have to say the intel pci express
even though amd is much better atm
Get an Antech Aria Cassis. it takes full height expansion cards and comes with a very good Antech 300W power supply. It also comes with a 3 year warranty. it is much better made than even the Shuttles. You get all the front USB, Firewire and 7 in 1 card reader. It takes up to 3 hard drives and 1 Optical drive. The Optical drive bay is coverd by a flip-down door, so it is the same colour as the rest of the front. you get a expansion slot VGA cooler as well. So you dont have your graphics card cooking like they do in all other Cube style Cases.
It will take any MicroATX mainboard. Then go for a Asus A8N-VM-CSM Nforce 430. It will give you HD 7.1 Sound and a PCI-E x16 slot. On top of that you get 1 PCI-E x1 and 2 PCI slots. To go with the motherboard I would put in a AMD Athlon64 X2 3800+ dual core.
The Case and Motherboard would cost about R1700.
Best of All, you can Upgrade anything in the PC since it uses standard parts. It will work out about R1500 cheaper as well
It is a little bit larger than the shuttles, but not by much. The shuttles are pretty big these days anyway. llok here to see the comparison: