Right-click on it's shortcut icon, go to properties, click in the Target box. (not the Start In box)
It should read "C:\Program Files\blah blah blah where Super Meat Boy is located.exe"
Add to that line -windowed -w #### h ####
for example
"C:\Program Files\blah blah blah where Super Meat Boy is located.exe" -windowed -w 1280 h 1024
If it doesn't work, fool around with the spacing of those latter tags, like
-w1280 h1024
-w 1280 -h 1024
-w1280h1024
Not exactly sure which works, but one of them should.
The first -windowed tab makes an execution override that forces the program to run in a window instead of fullscreen. This typically makes programs slightly more stable in the event of an error.