The most crucial areas in need of protection are the piston rings, cylinder walls, and valve seats. The enemy here is moisture, which can enter the engine from any of a number of places and cause serious damage. Since its not really practical to try and close up all of the possible areas of entry, we will concentrate on moisture proofing instead.
The first step is to warm-up the engine. This drives off any moisture that may have accumulated already and it makes it easier to get a good coating of oil in each cylinder. Turn the bike off and remove the spark plugs. Then, using a turkey baster, suck up 25cc's of engine oil and squirt the oil into each plug hole. Turn the engine over by hand (put it in top gear and turn the rear wheel) with the plugs still out to coat the cylinder walls, piston rings and valve seats. Then replace the plugs and drain the existing crankcase oil.
Next, fill the crankcase with fresh oil. I suggest you retain the old filter and plan on dropping this oil come Spring, but if you decide to use this oil after the thaw, you will want to change the filter now. The hard part of prepping your bike is now done and you can breathe a little easier knowing that moisture will not rust the piston rings to the cylinder wall. I just over hauled an engine that had been left unattended for a year and the cylinder wall was so badly pitted with rust that it had to be bored out 1 mm before I got down to good metal. Likewise the valve seats were a mess and I had to replace the head.
But we aren't out of the woods yet
The next step is to protect the inside of the fuel tank from rusting. Fill the tank to the top with fuel that has been treated with a fuel stabilizer. I have had good luck with a product called Sta-Bil, which you can get at any marine supply store, but any type will do. You also want to drain the float bowls by unscrewing the small screw on the carb float bowl. Any fuel left in the bowls for more than two months will turn into a jet-clogging sludge that will cost you a carb overhaul to remove. If you have a fuel injected bike then you can skip this step and move on to the next.
Because batteries self-discharge, it is necessary to keep it charged up when the bike is stored. The best way to care for your stored battery is to hook a Super Smart Battery Tender to it. The Battery Tender is one of the latest generation of "smart chargers." It will maintain the charge in your battery without any other attention from you for years. The battery can also be left in the bike. If the posts on your battery are corroded, now would be a good time to remove the battery bolts and clean them up. A little grease on the threads of the bolts will keep them corrosion free all season. Make sure you top off the electrolyte with water if your bike does not a maintenance free battery.
Get the bike, the rear of the bike anyway, off the ground. If you're lucky and your bike has a center stand, use it. Wipe all the bird doo-doo off and give the chrome the once over with a coat of polish to keep it from pitting. Wax the tank and squirt some rubber protector on the rubber parts to keep them from drying out. Make sure you wipe any smashed bugs off your fork tubes before you throw a tarp over the whole thing.
If you live where it gets really cold then you should make sure your coolant has enough anti-freeze in it to keep the system from freezing. It's easy to check the coolant with a hydrometer that is made specifically for this purpose. Bikes don't have freeze plugs like cars, and a cracked cylinder head is a very ugly sight indeed.
That's about it. If you live in an area where rodents will crawl up the tailpipe looking for a place to nest, there are rubber plugs available that you can by to keep them out. The are made for dirt bikes, but will fit any street bike. Also, when you're ready to bring your bike out storage, you might consider changing the brake fluid. It can pick up water from the atmosphere and it's a good idea to change it annually any way.
If you have performed all of the above steps you can be sure that the bike you store for the winter will start and run perfectly come spring.
