After seeing several examples of immaculate perfection in this thread, I started feeling a little self-conscious about my own cable management. Eventually, it bugged me enough that last night I decided to "rage" fix it. Here is the result:
Green: Cleaned up the two cables coming off the pump and hid them. Used a zip-tie to tidy things up.
Red: Swapped some cables around and routed the NB Fan out the back to the Case's fan controller. Cut and removed the rubber grommets after realizing there was no way I'd get them back in position with cables still going through them. They come out quite easily on this case which is odd because the grommets in a friend's NZXT Phantom feel a lot more secure.
Yellow: Brought the 2nd SSD from the top mounted drive dock (you can see the black SATA and SATA-Power cables at the top of the drive bays) back inside the case where it is significantly less vulnerable to theft. Not that any one would think to pop open that compartment or that the 64GB Agility3 is very valuable.
Blue: Took in some of the slack on the PCIe Power Cables to the 2nd GTX 480.