Well.
To start. You can lower the latency of your RAM by running the tightest stable timings possible. A lot of people will run something close to a 3-3-3-8 timing. But if you crank some voltage to your ram and run tighter timings like 2-2-2-5 you'll boost 3dmark scores. Another is to try benchmark runs with AGP fast writes on and off. Most of the time this won't make a difference, but in older systems having it on will speed your scores up some.
You can always slide your video card driver image quality bars to performance for about a 300 point improvement in 3dmark 2001 too.
A good defrag seems to help at times, and even if it doesn't help your score it should help regular windows performance.
I always like to shut every program I have running down while running a benchmark. No firewall or antivirus. Close my IM services. Turn the screen saver off, and set my back ground to a plain black wallpaper, that is, no 5MB jpeg's for a desktop.
Setting windows to 16 bit color used to make a difference for me too, but i havent tried it in awhile.
A lil' overclock on your video card or processor never hurt either. You don't need anything too radical at first. Just try it with a 5-10MHz increase in speed.
Nice motherboard btw Mini. It is a great board for tweaking.