Anyway, Laurijan, with your front panel connectors, have them run as close as possible to the "flooring" of the case, make them run vertically down the motherboard from their headers, then possibly hook under the motherboard; using the risers to support them. Its rather ugly to see two IO wires pop out of the middle of the case, tape them down to the floor if needed (of the top chamber of the case that is).
Fan wires, twist the wires together so they dont look like some random strands of wiring. Do that for the top two 120mm fans and the CPU fan.
SATA cables, route them horizontally, towards the hdd bay right of the connector, and make sure the wire is routed behind the bay, then "dropping" down to the hdd bays where it should connect; looks better that way. The sleeving isnt needed in this case for the SATA cables as it makes them look bulkier; somewhat worse looking.
I would with the audio cable try to also twist its strands, but this time slightly. reduce the slack in it so you see less of it from that hole.
Unplug that molex plug on your motherboard, as far as I know its only needed for SLi.
Twist the strands of the NB cooler together as well, for the same purpose
Try to make the 24 pin wire and the 8 pin a bit more concealed by using something to hold it in a position that makes less of them both visible via that hole.