I like to pull the spark plugs and lube the cylinders with fogging oil... then put plugs back in.
Also adding some fuel stabilizer (like Sta-bil) to your fuel tank is a good idea too... especially if you are running fuel with ethanol in it. And run the engine to get the stabilized fuel (or plumb in to a smaller treated gas can) in the VST and fuel lines.
And don't forget to remove your battery if your boat will be in freezing temps when stored.
Cheers!