I mainly use MTPaint, but also use the Game Maker sprite editor when it's something small and quick, or if I want to make a slight change to an existing sprite.
I used to use just the Game Maker sprite editor but then I learned the importance of shading and suddenly wanted something that could work with layers and defined color sets.
I also use Flash when I'm making Flash games, but I plan on not using Flash when making Flash games in the future since I suck at it.
