depending on where/how the tower is mounted, you could run a molex out the back or bottom and run the wires behind/under the counter top to a cathode kit.
If you want to play with leds, plexi would be the best bet in my opinion because if you shaved the tips of the leds and set them in plexi, it would be 2x the anti-directional support.. or w/e the heck you wanna refer to it as. Plus if you look at how the wood meets under the desk, there's a perfect gap to form a plexi shelf. The shelf would hold the wires up and the leds in and as I mentioned before, help spread the glow where as if you used something solid such as wood, the light would have nowhere else to go but straight (depending on how deep the leds were placed of course).
I threw something together really quick just in case people didn't wanna read. Picture should sum it all up.