Nuke pipeline:::
My first attempt at swapping out colors involved using a chroma key to pull out a specific range of color from images rendered out of Maya. This process was not as accurate as I needed it to be, and the result varied from image to image. I needed a pipeline that would work in all cases.
Next I tried limiting myself to three colors, RGB, and moving image channels around, which turned out to be faster, cleaner, and worked well enough for multiple cases. The unfortunate downside is that each image sequence out of Maya would be limited by these three colors only, and I would be forced to render out multiple passes from maya to give myself the texture diversity I want in the final comp. For example, the main character requires three colors alone, and does not share any textures with objects in the environment. He would be one pass out of Maya, each boxcar type would be another pass, the ground and railroad tracks might be another, etc.
Here is an example of this effect currently used today.
http://www.youtube.com/watch?v=rWtecq1hRDw&feature=related