I found that it's easier when you can hide and reroute the cables and wires. Then trying to keep the exposed ones parallel helps with the clutter. I built a Acrylic computer and that was a nightmare trying to manage the wires because there was very few places to hide with the clear case.
This is the first computer I built from a first gen Alienware case with the Hydraulic door that covers the drives. I filled in the badge and sprayed it in Black PPG Deltron base/clear coat. Then I added a full window on the right side behind the mobo and sandwiched in a translite poster from a Williams pinball machine's scoreboard with two cathode's as a back light. Homemade fan buss, fans and LED's had wires everywhere!