Gizmodo do a good job breaking this down, looking at the iPhone's new graphics chip - Samsung's PowerVR SGX GPU core - as a sign that one day, when the more powerful handset is also the most numerous handset, developers will naturally catering for the device that allows for faster, better-looking games.
Of course, this won't happen soon. There are already 40,000,000+ iPhone and iPod Touch devices out there, and it'll be a long, long time until the 3GS (and its successors) begin to outnumber them. To ignore that install base would be a little nutty. But one day - just like we see with PC hardware - they will.
In the meantime, though, we'll probably start to see more and more developers taking advantage of the 3GS' power by "sliding" their games, allowing those with a 3GS to enjoy better graphics, a faster framerate, etc.