Before I BOUGHT my computer, I picked up several books on how to BUILD a computer, and finally understood relationships between MotherBoards and Processors, and Power Supplies and everything else, and fans and cooling, and finally and having direct connection to the Mother Board as opposed to sharing Interrupts.
What I learned: (1) MotherBoards are fungible and few are made specially for manufacturers, so if you like a system, chances are you can get the same MotherBoard. (2) MotherBoards are the key to the system with set numbers of slots, USB connections, SATA connections, and other goodies such as built in video, sound and RAID; (3) Cases are proprietary. You might find a case which is similar, but not identical to the commerical computers; (4) Cases have everything to do with cooling and making the computer run well. If you slap a M/B in a case and the case is not well designed for cooling, you'll need more, or more powerful fans, and then more power supply. (5) I like horizontally mounted cases, e.g., rack mount, which make everything more expensive.
My vote is to BUY not BUILD a computer.