Usual stuff -
AGP aperture (depends on vid card mem).
For AMD64 set the HTT bus to as high as it will go.
Memory timings auto, but if option is there set the "Command Rate" to 1T
Disable any legacy (eg Comm1, Comm2, Printer etc ports you dont use).
Disable any IDE channels you dont use.
Disable drive detection for IDE channel where no drive is fitted.
I'm sure others can come up with more, this is just off the top of my head.