Your best tool for managing the wiring mess is to have a good plan of attack. Personally I like to start before I even have anything in my case. Sit down and find the strengths of your case. Where are areas that you can hide some wiring? Is there space on the far side of your case hidden next to the drive bays? What about an area hidden behind your PSU? Also take a good look at where the connectors are located on your motherboard. This will have a big affect on how you can run your wiring.
What are the weaknesses of your case and motherboard? Is there no place to run power cables behind? A Lian-Li case for instance can benefit a great deal from a simple hole near the psu to run wiring behind where the motherboard tray slides in. Find the weaknesses and plan out how you will get around em.
Plan out what power connectors you will need and use the bare minimum, then hide the remaining cables whereever you can.
After a good plan cable ties are your next best friend. Cable tie until you think you have done it too much and then do like twice as much
Many people like rounded IDE cables, but personally I find them bulky and depending on the cable they can be pretty inflexible. A ribbon cable can be folded and run flat against any flat surface in your case.
Another thing about IDE cables is that you want to use as short as you can to get the job done. 24" dual channel cables are a royal pain if you are running 1 drive that is fairly close to the connector on the motherboard.
As Stool mentioned its even better if you can run cabling behind your motherboard before you mount it. Thats one of the few complaints that I have with how I wired my last case. I have 1 wire that I should have run behind the mobo and someday it will annoy me enough that I pull it apart and do it
Split loom or cable sleeving will make things look alot nicer, although they don't really help organize much. When I have some free time I will certainly be sleeving my power cables on my newest machine
