Mate there are some great ways to tidy up those cables, let me link you to a few key items.
Firstly obviously good PET sleeving, you can find this @ any online shop for the most part....
Now for some instrumental things to a good clean case:
- small & medium black cable ties in 100 packs (4" for small works well, and 8.5" works well for medium) :
http://www.mcmaster.com/nav/enter.asp?pagenum=1431
- adhesive backed 4-way cable tie mounts in 100 packs :
http://www.mcmaster.com/nav/enter.asp?pagenum=1435 (Type "T" at the bottom of that page)
- helical cable bundling wrap (great for gathering large bundles of cable together in a single area (such as along the case floor):
http://www.mcmaster.com/nav/enter.asp?pagenum=772 (top of page)
With the combination of those things you can pretty much let your imagination run free as to how you can straighten things out inside your case. Those are the only things I use when I want a super clean professional cable-free look. Turns out perfect every time!
And if you have the time, dedication, know-how, and tools as Llwyd stated, cutting holes in the mobo tray for behind mobo cable routing is the ultimate. I did this on my phase changed rig and it turned out fabulous.
Here's a pic of that rig... Every single cable connected to that mobo was run behind the board, including the ATX cable, THAT WAS TRICKY! I could have done with shorter IDE cables but I didn't have the time to faff around with it so I just clumped em together.