This may be helpful to someone else out there. I had a rough time getting my PS3 controller to work with the non steam version.

I'm currently able to use it on my MacBook Pro through bluetooth with an app made by carvware called GamePad Companion. You can find the older free version of this app easily enough and it hasn't limited me with Super Meatboy.

The other piece of puzzle I needed was a dictionary of the PS3 controller's buttons:

#1 = SELECT
#2 = L3
#3 = R3
#4 = START
#5 = DPAD UP
#6 = DPAD RIGHT
#7 = DPAD DOWN
#8 = DPAD LEFT
#9 = L2
#10 = R2
#11 = L1
#12 = R1
#13 = Triangle
#14 = Circle
#15 = X
#16 = Square
#17 = PS Button
#18-19 = nothing

I still wish I could fullscreen the game though...