Check it out! http://www.youtube.com/watch?v=cHnd30No9M0
So the video demonstrates a game engine I started which is capable 3d tilesets along with full color and alpha channel.

It's programmed with C++ for Linux but uses libraries available in Windows (i.e., SDL) so it shouldn't be too difficult to cross compile. Anyways, here's the source code if you're interested: https://github.com/RabbitHare/scroller
In addition to the game, it includes the code for a level editor and a program to compile tilesets.