Another option is a recent ThinkPad, if you are considering a second PC or laptop. New ones (I've got a T510) run very, very quiet, thanks to owl wing-inspired fan blades and excellent heat sink/vent designs.
It's incredibly good at dissipating heat as well - the T510 remains cool to the touch when running at full stop, with only very slight warmth underneath the processor. The main intake is on the rear and the main vent on the left side, with many widespread intakes on the bottom as well. Setting it on your lap or a suffocating fabric doesn't make any noticeable impact to the heat level or noise.
I had an older Asus 900A netbook before, which ran very hot and noisy - not to mention slow. I know the newer netbooks are better, but I'd never get one with an Atom processor.
Other than that, the whole 120mm fans/water cooling, etc. recommendations are all good. A new case can make all the difference too, if you're using a poorly designed one.