To be honest I think one card that broke the format was Double Colorless Energy. Where would Luxchomp be without it? I know it would probably still be played, but SP in general would be nowhere near as good as they are now without it. A lot of stage two decks also have befitted a lot from DCE.
Other great sets include: Legends Awakened, (The Pixies) Stormfront, (Gengar, Gyarados, Machamp, etc...) Platnium, (SP engine+Broken Time-Space).