buy a realllllll big box/bag of cable ties (small and medium) and some "stick on loops" as mention'd above.
id start by unplugging every single cable and shifting the ones you can out the way or just dangle them around the side and out of the case. then start thinking of ways to route the cables as neet as possible, so if you have 2 cables that are going from the power supply to roughly the same place, cable tie them together a few times to keep em tight n close together. do it to all the cables u can. also as said above if you have the room then route behind the motherboard tray or you could put some behind the hard drive cage out of sight.
jus keep everything to the side and have nothing going across the motherboard (fan connectors etc etc) unless you really need to.
*edit* also i would put the fans on the top of the case to exaust air, not intake (unless you have tried both and intake turned out better)