finally I found out what to do
jscal -u 7,0,1,5,2,16,17,40,12,290,289,291,288,294,295,296,297,298,299,292,293 /dev/input/js0
First line does a remapping of the buttons and axis so that it matches the button and axis definitions of an xb360 controller as good as possible. Btw 7 means 7 axis, followed by seven axis ids, then a 12 for twelve button ids. You can should change that if your controller is not a Sony Dualshock 2 controller with adapter.
Second line tells SDL (used by super meat boy) to use that device with that buttonmap for input (the default is somehow different).
third line starts the game.
If you are interested in developing your own buttonmap for other controllers, feel free to post them here. jstest is your friend.
Edit: jscal -q /dev/input/js0 shows your current button mapping. here "man jscal" is your friend.