1) Six and one half dozen of the other, as the saying goes. On any modern system, the video card plays the crucial role in gaming performance. While AMD holds the edge in that department, it's overblown.
2) As mentioned, with the excepetion of Gigabyte you'll be hard pressed to find a compelling dual-BIOS mobo. Looking at each camp, here are some top choices:
Asus A8N-SLI Deluxe
MSI K8N Neo4 Platinum SLI
DFI nF4 Ultra-D
Asus P5AD2-E Premium
3) No, an AGP card will not work in a PCI-E mobo. There are hybrids out there that have incorporated both, but AGP performance takes a tremendous hit. It's not worth looking into.
As you've found out, AMD does not use DDR2. However, this is not a knock against them. While they could release a mobo that makes use of it, you wouldn't see any performance benefit on what's currently available.
Generally speaking, I favor AMD's solutions right now. Socket 939 will be around for awhile, PCI-E is available, SLI is an option, and most importantly they hold the price/performance ratio. If you have some time, read over this thread - LINK
. There's quite a bit of info in there for anyone currently looking to build and weighing their options.