except for PSU's (110V input in some places, 220/240V others) pretty much everything is standard.
dual graphics cards increases your total graphics processing power. it means people get higher frames per second, and can run at higher settings. nobody really needs it, and it is often expensive, however it attracts some people becaue they like their computer to be faster, and to get higher scores in benchmarks.
a PCI graphics card can be used in a system with an AGP slot. you just have to only have the PCI card in. although I would recommend staying with AGP if you can. or possibly PCI-E if you get a new computer.
as a matter of fact, PCI graphics cards are actually more expensive than their AGP equivalent. plus they are not as fast, because of the restricting bandwith of PCI