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I (re)built my own PC, after realising that the small case was the limiting factor in cooling my Athlon XP. I bought a lovely blue Chieftec case (so much nicer than the beige nonsense) and bolted in all my components, replacing my CPU cooler at the same time.
It does indeed give you a great feeling of satisfaction, and you have complete control ;-) The scariest moment is hitting the power button for the first time and seeing if it all actually works!
A *big* consideration for today's machines is noise. It really is possible to have a silent but powerful PC, at little more cost than normal. Go for all those clever Zalman heatpipe things, the Zalman flower cooler, a Seagate FDB silent hard drive, and choose your PSU very carefully. Between that lot, some acoustic deadener, and careful construction, you'll soon be zipping along in fast, blissful silence.