Posted by Don in another thread.
Here's what I recommend (and do in our shop):
1. Stabilize fuel WELL. Keep in mind, many stabilizers have TWO ratios listed.... one for everyday use, and one for seasonal storage. Use AT LEAST the ratio listed for seasonal storage (better to have a little more than not enough).
2. Run the engine under load, preferably in the lake, for 10-15 minutes. This will help to ensure that the stabilized mixture is completely through the fuel system.
3. Replace the water separating fuel filter. Remember to pour contents into a glass jar for inspection.
4. Fuel tank should be stored FULL, or BONE DRY (pumped completely dry). Keep in mind.... your engine requires high test fuel, so if storing full, be prepared to pump the tank in the spring before use (run it in your truck, which can likely compensate for any octane loss that occurred over the winter).
5. Change lower unit lubricant. Mercury or Quicksilver High Performance Lube.
6. Remove prop... inspect propshaft, and grease splines. Retorque to specs.
7. Grease all pivots on midsection of engine. Don't forget to grease the "balls" on the ends of the two short trim rams.
8. Inspect belt- look for cracks/wear marks.
9. Remove spark plugs... place 1 teaspoon of 2-cycle oil in each cylinder (same oil you're running). With the lanyard cord pulled (SWITCH OFF), and SPARK PLUG WIRES GROUNDED, spin the engine through a few revolutions (3-5) with the starter to distribute the oil evenly. Reinstall spark plugs. NOTE: If you replace your plugs annually.... I recommend waiting until you've run the engine for 5 minutes next spring (giving time for this "fogging oil" to burn away, so as not to "douse" a new set of plugs).
10. Remove hoses from any analog speedo or water pressure gauge. Blow backwards through the lines to expel any water, to help prevent freeze damage to the gauges.
11. Drain/treat all livewells, pumps, aerators, etc. as appropriate for your particular boat.
12. Store with engine in the FULL DOWN trim position.
Also, it's wise to replace your water pump in the spring before placing the boat in use. If can be done now.... but since impellers tend to "take shape" to their housing, it's best done just before placing the boat back in service.