If the bore is bigger than the stroke, an engine is oversquare. Conversely, if the stroke is bigger than the bore, the engine is undersquare. If they are even? Square.

As a general rule, engines that are "short stroke" are going to be considered those that are oversquare. In order to be able to turn at the RPMs that they do, the stroke has to be shortened enough that the piston acceleration will not result in enough force on the conrod, crankpin, or wrist pin to fail. If you imagine the piston having to change directions at both the top and bottom of the bore, and imagine two vastly different engines, one very oversquare, and one very under, the piston velocity and the acceleration felt by the undersquare engine is going to be much greater than the oversquare.

By shortening the stroke, you reduce the internal forces being transferred, and as such, allow the engine to rev out further. Once the basic operational parameters are set in terms of engine geometry, timing and port work can optimize the power output.

One of the biggest advantages of the short stroke engine is that it can often be made smaller than a long stroke.