AGP aperature size is under Advanced Chipset Options in my BIOS (Award). I did some research on this interesting issue in re to gaming yesterday, and there is no clear-cut answer. Much of the info you can Google is outdated and may not apply to contemporary cards, system RAM and operating systems. My advice is to keep tweaking it, play for an hour or so and then tweak it again, until something seems to work better than others.
Let me back up a sec and talk about what this setting is. The aperature size is part of the AGP protocol that was developed basically to help struggling video cards share the burden of complex textures with the system RAM. In other words, with the video RAM filled, some of the data could be shifted to the system RAM as relief. The aperature size is the amt of system RAM that can be allocated for this purpose. When the AGP standard was written, both commonly available video RAM and system RAM were fairly limited, so you had to strike a balance for best performance. For many people, these conditions no longer exist or have been substantively modified, so the old advice may not apply.
In my case, I have a new GeForce 6800 GT 256mb. My BIOS had been set at a default 64mb AGP aperature, and I bumped it up to 256mb as soon as I got the card installed. Several things that I read confirmed SK's comment that certain settings are good for max benchmarking scores, and others for optimal gaming performance. Opinions are all over the place, and you have to collate, synthesize and draw your own conclusions for your own particular system.
My conclusions based on what I read: 1) Most video cards have much more adequate memory now, 2) Using video RAM is faster than system RAM, and 3) Modern games are challenging video cards in different ways...not frequently requiring complex textures to be partitioned to the system RAM.
I took my aperature from 256 to 32 to 64 then back to 32. The differences were subtle enough to be my imagination. However, I felt like 32mb stuttered in game less often than the other settings. FWIW, the stuttering could be caused by brief server lag, latency issues or my cable node momentarily maxing out. The game didn't crash, and that makes me happy.
Some people advocated entirely disabling the aperature (setting to zero), but my current BIOS doesn't support anything less than 32.
Edit: I'm currently running 1gb system RAM.