If your main power cable isn't already sleeved, gets some 1/2 wire loom in the electrical section at Home Depot. Also pick up some electrical tape to wrap it with. If you have a window there are other things you can do, or you can order colored loom and use colored electrical tape. It won't hide it but it will make it look better.
For your other wires, if you have a space over or under or in between your 5.25 drives, you'll notice little cutouts on the drive bays. On the far side, bend one of these off and feed your power cables thru the hole. Then, run them down the side out of sight. Bring a wire thru here and there to reach your drives. You'll have to get creative, but it works. If I hadn't dropped my camera, I could show you.
As for fan wires, I took the 3 to 4 pin adapters and plugged them in behind the mobo wall and drive bay as well.
I then kept the fan wires tight and mostly out of sight as I found little holes to get them out behind the mobo wall.
At some point some PSU wires will be exposed as they are plugged into drives. Use the loom for that as well but if you are serious about this you might try this
guide to sleeving.
In addition to cleaning your wires up, if you are still using ribbons you should consider round cables for your IDE and Floppy drives. Reduces clutter and improve airflow.
Check out sites like
SVC and look under Wire Management to see some products for yourself.