Trying to learn how to optimize a custom-built PC

[AndyC160]

I built my current PC for gaming and school purposes about a year ago, and while everything has been running well I recently made the mistake of running the demo version of 3dMark06 and comparing my system's stats to those online...lol. Overall my system is considered average, but compared to systems with almost identical components I get pitiful results. (492 out of around 600 or so...doh).
My question is this: what kinds of optimizations can I make software-wise that would improve the way all of my components "work together," so to speak? The computer is my first build and so I'm sure that there are quite a few things I should have done differently, though I haven't had any crucial problems (melting processors, sparks, etc.). Is there anything online (or in a book, for that matter) that I could read up on to learn more?

Any ideas would be greatly appreciated;
-Andrew C.

PS: When I say software wise I don't mean spyware/junk/etc, I mean like configuration settings and such...

My basic specs:
Windows XP Professional
AMD 4800+ Dual Core processor
2GB RAM
nVidia 7800 GT video card
250 GB WesternDigital HDD

[Fatality]

When running a benchmark, is there unnecessary programs running in your background? Even thought your system is pretty powerful, unnecessary software running in your background slows down gaming and benchmarks. Open Task Manager and kill any processes unnecessary and try.

[pam123]

Were any of the rigs you're comparing the score to overclocked and do you have any interest in overclocking?
When benchmarking you shut off extraneous programs, if you didn't then Fatallity is right in thinking that's your problem.

[AndyC160]

I've thought of overclocking, but since I'm still new I figured I'd hold out on that one...although, since then I've got a room mate who's a computer science major, maybe he could help me out if I decided to do it. I'll try to do the benchmarking thing again without anything in the background, too. Thanks for the help!