Place the motorcycle on its center stand.
Thoroughly wash and wax the entire motorcycle. Run the bike until all traces of moisture are gone.
Don't drain the gas out of the tank. Instead, fill it up with the best quality gas you can find and add the appropriate dosage of a gasoline stabilizer (like Stabil). It's unlikely you could get all of the gas out of the tank, and if there's any water in the gas, it will be at the bottom of the tank and the last thing to come out. When you're sure you won't be running the engine any more, put a baggie across the filler hole and install the gas cap through the baggie. Set the petcock to “off” if you have a petcock. If your bike doesn't have an “off” position, make sure that the fuel cock lever is in the “on” or “reserve” position. If the lever is left in the prime position, fuel may leak into the engine.
Note: A word about petcocks- There seem to be two basic types: the traditional ON/OFF/RES type and the vacuum actuated types where the petcock is off only by the balance of a vacuum diaphragm and spring arrangement. Vacuum petcocks are a potential source of ON even if they aren't supposed to be. A little bit of leakage past these guys can gunk your carbs pretty badly. If I were the owner of such a petcock (attached to a motorcycle) , I'd disconnect the fuel line from the carbs and add a long length of plugged line from the petcock and route it up to the area of the mirrors and secure the line in place (note that hose end is not below tank level in event of problem).
Drain the old engine oil and replace the oil filter. With fresh oil, refill the crankcase all the way up to the filler cap hole. This step is necessary because the old oil contains acid, moisture and other contaminants that will damage the engine while it is stored. Run the engine to circulate the fresh oil and heat up the cylinders and pipes.
Note: Steps 4a and 4b are for protecting the top end engine components from rust and corrosion. Step 4b is to be used only if fogging oil is not available. Do either 4a or 4b, but do not do both.
Remove the air cleaner element. While the engine is running at idle, spray the rust preventative fogging oil into the air cleaner box. Try to give each cylinder equal amounts of fogging oil. Do this until the engine stalls or emits smoke.
Run the engine for a few minutes to get the stabilized fuel into the carburetors. Then, remove the spark plugs and pour 1 to 2 tablespoons of motor oil into each spark plug hole. (Clean the area around the plug of grit/sand/mung before opening the hole. I usually use Simple Green or GUNK on the spark plugs with the wires removed and heavy rinse during the wash to clean this stuff up. Some folks use compressed air. Be careful, a piece of sand under a valve could cause it to burn later.) Reinstall the spark plugs. Do not reinstall the spark plug caps at this time. Turn the engine over a few times with the electric starter. Now reinstall the spark plug caps.
Note: The sparkplugs and/or sparkplug wiring should be grounded to the frame/engine, otherwise damage may occur to the sparkplug high voltage wiring or the output side of the coils.
Note: You should consider having new plugs available for next year.
Drain the carb float bowls.
Replace hydraulic/brake fluid and bleed the lines. This is probably optional if you've recently done it, but if you haven't, the fluid will absorb 7 percent more water after your year has elapsed, and the water that's already in there will have had 12 months to work on the system components.
Remove the battery, trickle charge it to a full charge, and make sure the electrolyte is at the “full” mark. Make sure to remove the negative terminal before the positive terminal. This will remove the battery from the circuit and will eliminate the chance of grounding the positive.terminal with the screwdriver or wrench. Clean the outside of the battery with a mild baking soda and water solution and dry it carefully. Be sure not to get any solution inside the cells. Remove any corrosion from the terminals and from the wiring harness connections. Store the battery in a room that stays above freezing, off the floor, and preferably on a wooden shelf. Try to charge it every month or so, and keep the electrolyte level up. If you let it sit unattended for a year, it will self-discharge and may sulfate. You might set it up to charge for 30 minutes or so each day with a trickle charger attached to one of those 24-hour appliance timers. I'd be nervous to leave something like that unattended for a whole year, though. In any case, you shouldn't charge a battery in a place that doesn't have adequate ventilation. If the battery is already several years old and/or is using a lot of water, it probably won't be worth using in a year anyway, and you should consider buying a new one when you resurrect the bike next year.
Note: If the negative cable-to-frame is still connected to the battery but is unconnected from the frame for battery removal, then the free cable-end should be insulated with electrical tape or somesuch prior to battery removal; you don't want the positive and negative terminals to somehow communicate through the frame during battery removal.
Lubricate everything that might rust. Some folks spray 30-30 or WD40 on engine parts, exposed bolts/threads, etc. Put the appropriate preservative on leather or vinyl stuff to prevent drying and cracking . Don't forget to lube things like the cables, kickstand, sidestand pivots, suspension (if grease fittings), etc. If it's a chain-drive bike, liberally lube the chain.
Wipe down the fork legs with Marvel oil and leave enough to keep the fork seals moist.
Spray the unpainted surfaces of the motorcycle with the rust preservative.
Seal the pipes and air cleaner intakes with baggies/rubberbands.
Inflate the tires to normal pressure. If possible, prop the bike up on centerstand so that the tires do not touch the ground (this also takes the tension off the front fork springs) or touch it only lightly (if floor is concrete, put a piece of plywood under the front wheel) – this will keep the tires from developing permanent “flat” spots. Be sure that the bike is not stored near ozone-producing devices like electric motors (washer/dryer, humidifier, furnace, etc.). Ozone attacks rubber. With all this, you still might want to change the tires upon returning, as rubber hardens with age. If your tires are worn, just count on replacing them and don't worry about it.
Don't put it under a waterproof tarpaulin. Moisture condenses on everything under the tarp and promotes rust. Store it inside with a moisture-permeable (i.e., cotton sheet, cloth cover, etc.) cover on it to keep off dust, UV, whatever. If you have to store it outside without protection for a year, you need to do a lot of corrosion control on various pieces of the bike. The military would coat everything in “cosmoline”. You can use wax, Kalgard 30-30, WD40, etc., but you have to be careful about where you put the WD40, since its solvent eats some organic compounds.
Lock the bike the way you would if you were going to leave it unattended for a long time, since you are. Find out if your insurance covers theft or fire damage. Most homeowner policies don't cover motorcycles, and you have to buy special coverage for your bike.
Write yourself a detailed note concerning what you did, and what you need to do when you return, and leave your notes with the bike. If you took any parts off, put them in CLEARLY labelled containers, and place them with the bike (in the same package, hopefully). Upon your return, if you have a service manual (if you don't, get one now and leave it with the bike) look at all the stuff that's supposed to be replaced every two years, and see if it needs replacement (hoses, etc).
Pat the tank and gently kiss.