The nice folks over at Apartment Therapy have several entries on how to deal with cable clutter. I've linked one below and here's another:

http://www.apartmenttherapy.com/untangled-organized-creative-c-164296

Search on "cord control" on their website for more.

Also, check out Ikea. They have some boxes that attach to the underside of your desk to hold cables, as well as lots of other cord control measures.

In your case, since it sounds like the desktop will be attached to the walls, can you get some electric outlets installed so that they are just above the height of the desk? That way you won't have to drill holes in the desk for the computer cables to run through. If you can figure out the best placement for the computer, you could even hide the outlets behind the computer. Then you'd just need to bundle up the extra cable so it isn't taking over your desk.

Here is a link that might be useful: cord control

Camlan, can you point me to the section of the Ikea website that has the cord control items? My searches are coming up blank.

The items that are sold for cord control on the Apartment Therapy link don't come close to fixing the problem for desktops. There are so many cords running in so many directions that the best I seem to hope for is to loop the excess. And as soon as I do that, I find that I have to access something and all my nicely bundled loops have to be undone.

Graywings, try searching on "cable management" on the Ikea site. But that search doesn't seem to pull up everything they have, unless they've discontinued some items this year.

Also check out the Ikea Hackers blog. Search on "cable" and you'll pull up lots of posts where people have come up with solutions for the cables.

And do go back to Apartment Therapy and search on "cable control" or "cord control." There are hundreds of entries with various DIY or purchased solutions.

My own solution for computer cables is a) an iMac (just has fewer cables and also has cord control built in) and b) an old desk with drawers and a "modesty" panel, so all I have to do is drop the cords behind the desk and they are hidden and c) wireless router and printer, to eliminate a few cables.

My one tip is to label all the cords with what they are for. Saves a lot of time and bother.

The ThinkGeek website also has a few options for cable control.

(label both ends of the cord using a P-touch label)

Google searches will turn up lots of things that are sold for this--cord covers, wraps, etc.

I like the double-sided Velcro wraps (Home Depot has them) for making the loops--easily done and undone, unlike cable ties.

And I like the grommets we have in the desks at work; they let us put the wires underneath, yet pull them up or down.

And mounting a basket of some kind to the underside of the desk would let you put the bundles of extra wire there.
Or an under-the-desk wire tray:
http://cableorganizer.com/under-desk-wire-tray/?green=11983999413

And here's a great product!

http://cableorganizer.com/Wiremate/?green=11983999413

Here is a link that might be useful: CableOrganizer.com--just the site for you!

More gadgets from the Container Store!

Here is a link that might be useful: Cord Control at the Container Store

They also have cords that have like 10 spots to plug things in.Has a switch to turn all off,good in case lightening hits.

i have a large builtin desk in the kitchen where i have a desk top computer, printer, etc...

it is built so that the area where the chair goes is open to the wall behind it and is flanked by cabinets on either side--the cabinets and the desk top have the cord holes and the outlet is on the wall where my knees are---i had lots of cords dangling back there and what i finally did to manage them was put up several of the small command hooks-high and out of sight---the wires are still a mess, but you can't see them!

I stumbled across the Quirky web site recently. It has several solutions for power cords and too-long cables. Check out "Power" and "Cord Management" and "Cordies" for some ideas.

Here is a link that might be useful: Quirky

This does not address the OP but about 10 years ago I was doing a lot of work in Berlin, Germany. One office was having an open house to celebrate the company's 10th anniversary. I was surprised to see NO cords dangling from any desk top and asked how they did it. My colleague sat at the nearest desk and showed me how the top slid toward him revealing a gutter at the rear where all cables lay and were then routed through a hollow back leg of the desk. This was 10 years ago and I've never seen this in the USA. Desk surfaces were remarkably clean and even desks in the center of their open-concept office were starkly tidy. (It was Germany, after all. Even their pencils appeared to have been arranges with a ruler.)