From the blog:
You can now customize the controls of Meatboy himself. This customization only applies to Meat Boy since it's the most important aspect of the game. There is a file in the install directory called "buttonmap.cfg" (It was buttoMmap.cfg when I first uploaded it...I was quite tired). So it works like this. There are two sections in the file, keyboard and gamepad. You can set the movement, jump, and special / run keys to anything you like (within reason) through this file. So you lefties that wanted WASD, here you go. The config file is case sensitive, so just make sure its all lower case. Some buttons that do not have alphanumeric represtation have special names like:
Left Shift: shift
Right Shift: rshift
Left Control: control
Right Control: rcontrol
You can only bind an action to one key.
For Joysticks you can customize the jump and special / run buttons by putting in the button number. For instance, the default is set to 1 and 3, which correspond to A and X on the Xbox 360 gamepad. 1 and 3 correspond to the equivalent of B and Y on Logitech controllers. To look up the button numbers for a gamepad (if they aren't written on the buttons) just go to Control Panel and look at the Game Pad properties.
There is another option called useanalog. This is set to true by default. This property allows the game to use the joystick as the dpad. If you are experiencing weirdness, set this to false and it will disable it.
Note: These controls only affect Meat Boy, Menu's are hard coded with controls.