that all depends.. im assuming you are going for quietness.
if you have a modern process that runs at a low clock rate, you may be able to get away with one of those fancy "fin" heatsinks as shown on toms cooler roundup.
of course if your using a top of the line processor at high Mhz forget it.
but you could use a big heatsink with a small slow fan, or go for one of those nifty silveraado's. nice and quiet
thats assuming you want a quiet computer....
"Don't be too proud of this technological terror you have created"~Darth Vader, Star wars