I guess since you mentioned the Matrix, that would be your fav movie... Not a bad place to start, although it has probably been done to death...
Since most of the Matrix theme stuff has black and green, how about a black glossy paint job, with green characters scattered in random places? Green LED fans, IDE/SATA cables, LEDs for the front, and maybe green UV paint for the window (I'm assuming you want to do a window)... Or even UV reactive green everything for the innards...
Fot the window, you could etch/engrave/whatever the inside surface with the characters (if you didn't put them on the outside panels), or whatever Matrix-inspired graphic(s) or text you decide you like best.
Another point would be to show more pics of the case, such as both sides, front, top, inside, and back... Perhaps put it all together and take some pics of the insides, fully loaded, as a basis for people to offer suggestions
Above all, I would look at cases in the
PR Gallery for ideas... This case is going to be YOUR baby, personally, I would think you'd want to show off your case, after it was modded to YOUR liking... What's the good in modding a case according to other people's ideas of what looks good/cool/whatever if your creative genius wasn't put to work? Just my $.02, for free...