The best solution to cable management issue is velcro cable tie rolls Amazon.com: Velcro Cable Tie Roll, 3/4" x 5 yards: Electronics
You take a roll of this stuff, cut it and wrap it around your cabling. The advantage to the velcro is that if you later need to remove it, or add a wire, etc...you don't have to cut it like a zip tie...but instead just open it up, add to it and wrap it back on itself.
My second trick is to use colored electrical tape to hold down small wires and such. Just tape them to the side of the case in a non-obvious location. Helps to keep them tidy and looking sharp. Also, you can use it to bundle a couple of small cables together. I don't wrap the wires from end-to-end, but rather just tape them every few inches and I use a very small amount of tape.
The third trick is simply to take lots of time. Getting a good cable job simply takes time to think it out and run the wires properly. I probably look at the case for up to 2 hours just placing parts and thinking it over before I even start to permanently mount anything and clean up the cables.