World Superbikes are based on production motorcycles. They have to be homologated to be allowed to race in the series. That means that the manufacturer must have made and sold a certain number of the streetbike to the public before they can use it in the series - cuurently that number is 1000. From 2010 it will be increased to 3000.
MotoGP on the other hand is the "Formula 1" of motorcycle racing. The machines are not in any way production based, they are special purpose-built racing machines.
World superbike currently allows 1000cc engines for multi-cylinder machines and 1200cc for 2-cylinder machines with some additional restrictions. This increase in capacity was instituted to allow the Ducati 1098 to be included in the series.
MotoGP has previously been limited to 500cc 2-stroke engines, then 1000cc 4-stroke engines, and now is 800cc 4-stroke.
In general, the level of technology in MotoGP is some years ahead of SBK and the machines are a lot faster.