It's definitely more expensive. At the moment it's not any better (or cheaper) if you have a top card like the Sapphire X850XT AGP Platinum Edition (also in PCI-e), which beats the nVidia 6800 Ultra!
Both come at a premium though, X850XT from $440.-, 6800 U from $375.-
To answer your original question, the AMD64 has better memory management and runs in Dual Channel mode.
An AMD64-3200 will 'run/walk' circles around your XP2800+, (depending how 'good/bad' your current mobo is.