the 9600 gt was using beta drivers so it's possible that the drivers helped it out a lot. other speculation focuses on some sort of mysterious architectural improvements. All things being equal, you'll get better performance from the 8800gt at higher resolutions with the same drivers, but the 8800gt will cost you about $30 more to buy. BFG,keys, and some others ran a lot of tests in some other threads. One thing that I got out of those tests was that shaders are great when you have enough but that performance can really tail off quickly when you're running out of them. The vast majority of the benchmarks that were run by the various websites didn't stress the 64 sp's of the 9600gt enough to highlight its weakness. Depending on what games/resolutions you play now and in the future, you might or might not ever see a significant improvement by using the 8800gt over the 9600gt.
Looking at a number like "85-90%" makes you think that they are comparable cards. What they really are is more like even at lower resolutions, 10-15% advantage for 8800gt at middle res, and a BIG advantage for 8800gt at higher resolution. It's like comparing michael jordan to allen iverson. They both have unbelievable stat lines for their careers, but as the resolution/pressure ramps up, which one do you want on your team? If your team sucks and is always going to be an also-ran then you're better off with iverson b/c he's a lot cheaper and will still fill the seats. If you want to win the title then do everything you can to get jordan.