vista gpu: you'll need direct x9.0 h/w support in the GPU.
on the ATI side, the radeon x800/x1800/x1900 series with at least 128MB of RAM will be sufficient. 256MB will be better. i would avoid radeon x1300s.
for nVidia, geforce 6000/7000 series with 128MB of RAM is needed. i would avoid the 6200s and 7300s.
PATA drives: your PATA 'ports' on the mobo each support two drives with the proper cable, so 2 PATA channels support 4 drives. retail drives usually come with the proper cables. put the HD on the primary (typically IDE 0) port, and the DVDs can share the secondary port.
1) Are there any GPUs available now that will allow me to take advantage of Aero (or whatever that 3D Vista desktop function will be called)? Nvidia cliams that its GeForce 7 series is ready for Vista but... with Vista so far away from release, how can they be sure? I plan to get a powerful GPU now and SLI it later. But if I'll have to wait until the DX10 cards, then I don't want to waste my money now.
2) What's the best way to connect 3 PATA drives with only two PATA ports? I'll have DVD-RW drive, DVD-Rom, and a 300GB ATA-100 HDD. I've heard that placing a optical drive and HD (master and slave respectably, or vice versa) will hurt performance.