This is something else entirely but... There's an interesting DS game coming out called Drawn to Life where you pixel in your character and it slaps it onto a 3D cubethingy, turning it into a playable hero for an RPG.

I was just playing on the flash demo. Made Batman and some limbless creature too. I'm not sure how intricate and accurate the actual application will be... we shall see. For one, I hope there's a tool that lets you move around the screen when you're zoomed in all the way (or I'm just missing it). It's still neat that someone finally did this.

Ugh, I tried that thing online, it's completely ridiculous  I wouldn't consider that game a pixel art program at all of course, because you just have to draw your character; the rest of the game plays like an adventure game.

Confirmed characters:

Pit
Mario
Link
Kirby
Pikachu
Fox
Samus

 

Don't forget Metakirby, Solid Snake, Zero Suit Samus, Wario, and all the characters from melee...

EDIT: lol, looks like Malor beat me to it. Oh well, I added a few more.

Sorry, but this is definitely not finished. It lacks proper shading, texture, and anti-aliasing. Don't mean to sound rude, but this really needs some more work.

I've always wanted a handheld device to do pixel art on...good thing I have a DS. This could be really cool! I just wish a big company would do something like this.

Personally I much prefer the mouse aiming games, but whatever floats your boat I guess.

I also think the atmosphere is quite nice. Also, I like the great level of contrast between ground and sky; very good to have in a game. Two crits: the enemy is very difficult to read, I'm not even sure what it is. Also, the HUD should be bigger in my opinion, and try to be more creative with it as it looks boring at the moment.

Overall, very nice work, looks like it would be a fun game to play.