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Here's a link to the LED's I used:

http://superbrightleds.com/TriColor%20LED.htm

They're a common anode RGB LED. Because the cubes are small and only 3in^3, I didn't need 3 separate LED's. I've pointed the LED's down at some tinfoil, and they look great with the top cover on.

I also decided to use SIPP sockets for the LED end of the cable. Grant recommended those, which is why I chose that. I found that its quicker to just put the LED straight into the SIPP socket without rearranging any of the pins, and then just rearranging the wires on the cable to line up with the correct pin.

For the other end of the cable where it plugs into the boards, I actually couldn't find a header that I liked to plug into the pins. I ended up using a .1" k.k. connector (Mouser part #538-08-50-0005) With 4 wires per cable that equates to 512 of them.

Data sheet for .1" k.k. connector:
http://www.molex.com/pdm_docs/sd/008500005_sd.pdf

I'm using the WashU software, which is running on Fedora Core 4. I actually also have your software installed on the windows side. (I have a dual boot with FC4 and Windows) Ultimately, I'll end up using whatever software fits my needs. My main concern is having the ability to resize the animations for my bar. My bar is 1/4th the size of everyone else's design, so only 1/4th of the animations will show up on my bar. So who knows... I guess whoever implements that is who I'll probably go with. (no pressure of course) :-)

I definitely agree that making all the cables is hell^H^H^H^H very time consuming.

Best of luck!!!