6800 GS is newer, more advanced, the GT is more powerful by nature, it has 4 more pipes, i'd get the GT
They generally use the same core, so no, its not more advanced. The GT has 4 more pipes, and the GS has a higher core clock to offset the gains. In most games/benchmarks, they trade blows, but are generally within 1-2fps of each other. They're near clones in performance, and the GS is cheaper. The GS is also an unbelievable OCer, not sure on the GT in that regard myself.
The AGP GS is clocked the same as the GT, so if you're limitied to AGP, get a GT instead. For PCI-E, get whatever you find to be cheaper, which is usually the GS.