I think a well-maintained original console is the most valuable. I've also seen some WTF paints and cuts that in my opinion removed almost all value from the console. On the other hand, I've seen some really nice mods, like a Mario cut into a NES console. It was obvious time and planning had been involved and the case was very nice looking. I modded a 2600 Heavy Sixer by stripping the wood grain and bezel paint, and it is now all black and beautiful. Something I wouldn't have done, except the wood grain was badly faded and scratched, and in that type of case, I don't think there's any way to restore wood grain. In that instance, I think I actually increased it's value.
My summation, if you're going to cosmetically mod, have a good reason, or at least a good artistic idea, plan appropriately, and take the time to do it right. Don't just toss a can of spray paint at it and expect it to be called it a masterpiece.