I'm not sure about pure graphics performance, but the one with the NVIDIA 9400M is one generation newer. So that iMac has more recent features, such as a Mini DisplayPort instead of the Mini-DVI port and support for up to 8GB of RAM versus 4GB (6GB unofficially). The NVIDIA 9400M supports OpenCL in Snow Leopard (this is the technology that allows the GPU to do non-graphics processing); the Radeon 2600 Pro does not support OpenCL.
On the other hand, the newer NVIDIA 9400M iMac uses
integrated graphics. That means it uses system RAM for graphics. Although it has good performance, the older Radeon 2600 PRO iMac has
dedicated graphics (and slightly faster clock speed), so its overall performance may be better (not counting the future potential impact from OpenCL and higher RAM limits).
You can compare the specs in more detail by reading the profile pages for the two models here
http://www.everymac.com/systems/apple/imac/index-imac.html