DDR2 has faster stock speeds than DDR1 RAM, I believe that they've hit 800MHz with DDR2 but I'm not certain. I know for a fact they at least have DDR2 667. However, DDR2 has much higher latencies than DDR1 RAM, and costs a helluva lot more.
DDR2 is an Intel only platform at the moment, if you are buying an LGA775 system you will be using DDR2, and any other socket will use DDR1. There is no choice between the two.
In my opinion, it would be best to get a cost effective Athlon 64, 3000+ is dirt cheap right now as is DDR1 compared to DDR2. Hypertransport bus makes up for the DDR2 bandwidth with speeds up to 8.4GB/s.
Intel C2D E6320 / AMD Athlon X2 3800+
Gigabyte 965P DS3 / DFI nF4 Ultra-D
2GB OCZ Gold PC2-6400 / 2GB OCZ Gold PC4000
eVGA 8800GTS 320MB / eVGA 6800GS 256MB
150GB Raptor / 74GB Raptor
2x500GB / 320GB
OCZ GameXStreme 850w / OCZ StealthXStream 600w