I've spent some time this weekend working on adding support for gamepad controllers :) You can test it out on the Super Mario Bros prototype and Las Vegas. If you do try it out, I'd appreciate some feedback.
I've used the standard HTML5 Gamepad API, so it should work for most controllers.
You can view the default gamepad assignments in the game settings [F3] , or by hovering over the button with your mouse.
To change a gamepad assignment, click on the name of the button in the game settings (it should start flashing) then press the button on your gamepad to assign. It should show the number (or arrow in the case of directional buttons) associated with the button on your gamepad. I've left some functions (like Start and Select) without a default assignment, but you an assign them to your gamepad if you like.
The Gamepad API unfortunately only identifies buttons by number, and which button is assigned to which number will vary by manufacturer, so there is no easy way to display the button names or symbols. But if you hover over the gamepad icon in the game settings, it will show you the ID of your gamepad. There is a possibility I can then, based on that ID, map the numbers to button names (or symbols). If you'd like your controller mapped then let me know and I'll give you with details of what to provide.
I've also added a "Reset" link so you can restore the default assignments (for both keyboard and gamepad) in case you run into any trouble.