I came across this website which allows you to custom color a BMX bike. This isn't some Republic-Bikes-choose-from-these-5-colors type of customization. Full color charts on everything from the spokes to the bar end plugs!
The bad part about it is that you can't order the bike once you've designed it. You can, however, order a custom painted carbon fiber Trek Madone through their Project One Website and even get some Nike's to match through the NikeID Website.