Add a fuel stabilizer to the gas tank. Completely filling the gas tank with fuel will also help as having air in the fuel tank is a big contributor to fuel oxidation.
Fog the engine down or put a small amount of oil down the spark plug holes.
Remove battery and store it in warm dry place. Attaching the battery to a battery tender or low amperage automatic charger will help keep the battery in good shape for the next season.
For areas subject to extreme cold and/or extended periods of frost, you may also have to add anti-freeze in the water jackets. Refer to the owner's manual for additional tips and guidelines for winterizing your watercraft.
Footnote Reference: Watercraft Tuning Tips and Tricks