I think that we upgrade way more than most people. If you don't upgrade often the pre-builts are the better deal. As we build more over time we accumulate things like extra cables, fans, screws and stuff. If you only upgrade every 3 years you don't get that stuff.
Also after 3 years there isn't much that can be used on the new system. Floppy,and CD-ROM. With a few maybies thrown in: case/PS, Harddrive, speakers.
So there usually isn't much money to be saved by not going pre-built.