The most basic difference is the length of the muffler section. Short Megs have a 14" muffler. Street Megs have a 20" muffler and use the passenger pegs as a mounting point, similar to the stock exhaust.
Obviously, the Short Meg will be a bit louder. The Short Meg can drag the ground in hard lean angles. The Alien Head is basically the same setup, but with a slightly different shape that allows better ground clearance.