http://teknopants.com/pixothello/
Very useful tool. It is kind of buggy though (With my experience, DON'T use the bucket tool, and be sure to always check what tools are selected) Not only can you use it for tilesets, you can even make animation with it. Its a bit complicated and hard to understand at first, but you'll get used to it and create some cool things. Here is 2 examples, of what I made with it for my own game.
Tiles 1
Tiles 2