If you got a free optical bay, iyou can hide some there. Also there is an opening next to the PSU bay, you can bring in small wires there. I believe everything except the mobo 24-pin plug can be pulled there. Also nothice that bar that crosses from front to back, you can see from outside, the PSU it on it, there is a space there, you can drag some cables whichever you think you need. Then its just a matter going over that rear 12cm fan, and some cellophane tape will work, and will not be noticed. When I have time, I'll try to drill some holes on the mobo tray, and try to pull the IDE wires, and all other junk. Actually my wires are very cluttered, just a matter of not noticing it. I got a hardcano 12, more wires.
Another thing is below the removable hd area, there is a small space, good for IDE wires, and other junk you want to hide. Also the back of the tray, where to power to the front panels go, there is lots of space for manipulation. Also save those metal-plastic wire tying things when you buy stuff. Come in great use. For the other wires, its just a matter of making origami shapes and compacting at the drive. Will not work with rounded cables. I think thats it.
Mine is still messy...

Wow, finally you got the job done! It looks so tidy and nice.