Newegg sells a pack of multicolored zip strips. Use them liberally (like ever 2-3 inches of wiring) and use some round ide and floppy cables. Do this with every wire in the case. I also take excess cable and zig zag it into a bundle and put two zip strips on it. I have about 5 inches of wire from my cpu cooler to the motherboard plug..the actual distance is about two inches so again I zig zag it up and tie it. Trim all the zip strips with some dykes and you're set. Take unused power cords & connectors, bundle them up, zip tie em and tuck them away in the extra space by your unused 5 1/4 bays.
It's all about time spent and attention to detail. You can make it look really good and believe it or not drop the internal temp on your case a few degrees.