You said you want to go with an AM3 setup. Good choice. I just built a new system and while I was building it I considered several options to keep the cpu cool.
I decided to go with a Musscool Water Cooling System and I got it at Fry's for les than 65 bucks!
It has a very small footprint(Doesn't take up much space) and installation was quite easy.Goto photo bucket.com and look for airwolfflies photo album and you will see what my install looks like and there are detailed pics of how it fits inside my mid tower case.
My setup consists of the Asus M4N78 Pro mother board, 6GB of DDR2 RAM with a Cyclo Cooler for the RAM, 1GB Nvidea 9500 GT video card, Liknsys PCI wireless card, 1TB SATA HD and the Samsung 22X Speed plus burner.
My cpu has never been beyond 32C with the Musscool cpu cooler and I know if you get it for yourself, you will be glad you bought it.
Hope my suggestion works for you.
airwolfflies.