The best upgrade I ever did was actually a "downgrade". After my 66cc bike got stolen, I built a Skyhawk frame with a 48cc engine. The 48cc is so much smoother than the 66cc. It also (weird, I know) feels like it has the same amount of power. Maybe because I ported the transfer ports before running the engine.
Anyways, I feel as if I had balanced the 66cc engine that I could have actually made more power. It just felt like the engine was ready to shake itself apart at high rpm. There's a how-to on this website, along with some other good tutorials.