First thing you should do is take apart the computer, give it a good cleaning. If that doesn't help, or your still not happy with it, look into some new parts.
What kinda parts. Well first is fans. You want the most CFM (Air flow), with the least DB (Noise). There are some fans out there that have a really high CFM rating, but also have a high DB rating. These fans are good if you hook them to a speed controller.
After that, you'll want to look into dampening vibrations in the case. Vibration=Noise. I like kits like these, they make things very easy.
You can also upgrade the CPU heatsink, and VPU heatsink. I like the ones made by a company called Zalman for CPU heatsinks, and Arctic Cooling for VPU heatsinks.
After that, you can pad the case with foam. You can put it on anything but PCB boards! Theres also stuff like Dynamat that can help also.
Past that, your getting into really modding the computer! Cutting fan grills out, making wierd rubber-band hard drive holding things. Watercooling, and other wedgits.
Heres a video from the good old days of The Screen Savers. A Silent PC project to be exact.
If you need help with anything, you can PM me, I'll do what I can.