In the orginal boxes if at all possible. Of course, if it's self-built you won't have one of those nice heavy boxes with the molded styrafoam for the CPU, but you may have one for the monitor.
The suggestion to ship the drives seperately is probably a good one, as is taking off a heavy, clip-type heatsink.
When you pack the CPU, you want to arrange packing material to transfer any loads around the computer case, instead of through it as much as possible. What I mean here is that if something heavy gets stacked on your box, the packing supports it instead of the computer.
And, IMHO, do anything possible to avoid shipping it via UPS. Every package I get through them is damaged to some degree (the packaging, not neccesarily the contents), and I've had one that was literally driven over (you could see the tire marks).