Hello everyone I'm new is just starting to use these modeling software Mudbox for example, 3DSMax sketchup and I used it as a graphics engine CryEngine 3 free sdk
http://student.gamemaker.nu/~patlil030/projects/ninjapirate.htm This is a prime example of how an indie game can be purely awesome. Great fun, awesome visuals, and it's made in GameMaker.
Also wanted to add to @William3DArtist answer. You can create an additional channel that is custom one User0, User1 etc and put it as an extra export map. I used this a lot because needed masks exported from specific textured regions and use it later in shader, because of the amount of iterations, that gave me automaticy…