3DMark has become somewhat of a standard these days, but because of some shaky business practices its becoming less of a way to compare different system components but I believe it will work well in comparing different settings with the same hardware.  According to testing 3DMark 2001 performed the best at 256Mb AGP Aperture size. and 3DMark 2003 seems to perform the best at 128Mb AGP aperture.

With all of the complicated textures in Code Creatures I was sure that the score would go up as the AGP aperture did and I was right. It looks like this benchmark scores better with more texture memory and less system memory.

GL mark is a program similar to 3DMark but is for testing Open-GL. To tell you the truth it doesn't look like it has the budget that 3DMark has because the program tends to be buggy but I was able to get a good idea of performance with it. According to my testing, GL Mark performed its best at 256Mb AGP aperture size.

This benchmark may be my most hated test just because of the work involved in using it.  This is due to the amount of time it takes to run the test at different resolutions.  Below to save space, I just posted graphs of 640X480 and 1600X1200 all the resolutions in between showed the same results. I would say that AGP aperture has little to no affect on the outcome of this benchmark.