I have seen cables (hdmi) that are designed for this sort of thing...they come in parts (end plugs and main cable) with ps/2 style connectors. So you run the cable through a conduit, and plug the end-pieces (with the appropriate termination plug) onto each end.
There's nothing really special about the wires in a usb cable though (unlike cat5), so your best bet is to simply buy the appropriate length cable, cut one end off (leaving several inches of cable on the plug side), run it, and then splice it back together.
-Margrave
(edited for clarity)