I think the best thing you can do re: cooling, is pick the right case. I am a huge fan of *quiet* computers, so I looked around forever and finally found this:
Antec.com - Performance One
It's pricey, but it's designed to be quiet and keep stuff cool. I have two fans in mine, both blowing out (one out the rear, one up), both 120MM and very quiet. Seems to work very well. My computer is in a desk too and my video card is passively cooled.