Wash & wax. Then:
Change the oil. Don't store your engine with dirty oil that's laced with contaminants. Many claim that dirty oil produces acids that can harm your engine during storage.
The last thing to do on your final ride for the season is go to the gas station, put Sta-bil fuel stabilizer in the gas tank, fill the tank, then go right to the parking spot. A full tank will help prevent condensation (water in gasoline) and the Sta-bil will keep the fuel fresh until spring. It's important to put the Sta-bil in immediately prior to filling it because 1) you want it to mix with all the gas, 2) you need to run the car a bit (the ride home) to make sure the Sta-bil/gasoline mix makes it all the way through your fuel system before you park it.
Gold Eagle - STA-BIL
Whether you leave the battery in or not, make sure you hook it up to a Battery Tender. This is more than a charger. It cycles the battery so it keeps it's performance at it's max. Make sure you get one for a 12 volt system.
Batterytender.com - Home of All Your Charging Needs Battery Tender PLUS! - 12V @ 1.25A
Personally I park the car on "Flatstopper" ramps. This prevents flat spots forming on the tires. Make sure they're properly inflated and periodically check them over the storage time.
Flat Stoppers - Race Ramps
Get some silcone grease such as Sil-glyde. Apply it to the weather strip around the doors, trunk, and hood. The last thing you want is to open the door in the spring and have the weather strip tear apart with half of it stuck to the window.
Amazon.com: SILGLYDE LUBE COMPOUND-- 8 OZ.: Automotive
Stuff some steel wool in your tail pipes, especially if you're storing outside. This will keep mice from nesting in the exhaust system.
You should probably cover the car, but I don't know anything about car covers. I'll leave that for someone else to expand on.
