In Shutterfly, when you go to order a print, choose the option to fix/crop your photo, select the crop tab, and select the custom crop tool. There's an option for a square!
ETA: You're limited to print sizes of 4x6 or wallet in Shutterfly, which means your finished square will be approx 3.5x3.5 or really teensy. You could also crop in iPhoto, and take it to a local photo lab for more custom printing.
mom to Emma, s/b 11/04/04
and Max, edd 01/15/06 - it's a BOY!