Some engines have a lot of unused potential displacement left there for future factory improvements. Higher displacement usually improves the power output of the engine, but often causes it to only run well on higher octane gasoline.
Displacement can be increased by replacing the engine's stock crankshaft with a larger one, which not only pushes the piston up further, but pulls it back down just as much more. Other parts that can be changed to improve compression include pistons and piston rods.