The GTS is a G90 and the 9600GT is a G94 so they are quite different. Basically, the GTS will have a larger memory bandwidth (better for higher resolutions), but the 9600GT will probably perform equally well at lower resolutions. The benefit of the 9600GT however is the PCIe 2.0 compliance, thus giving you increased performance in the future.
So essentially, assuming you have the PSU to cope, go with the 9600GT unless you have crazy big monitor...
BTW synthetic benchmarks are great for comparing synthetic benchmarks (LOL). At best, it may be worth changing the settings to the actual resolution you will be playing games at, and comparing the scores. Other than that, try the Crysis bench as well.