Everyone's got their own opinions on this subject, here's mine!
Add STABIL or a similar fuel stabilizer to the tank. Run the engine, or ride, for long enough to fill the carbs with the treated fuel. Best is to then shut off the gas from the carbs and either drain them if they have drain screws, or if not, run as much gas out by running the engine as possible. This reduces the amount of fuel that will evaporate over storage. Ideally change the oil immediately before storage, so the oil is in the best shape to protect while the engine sits.
Remove the battery and keep it on a "smart" charger, one that can keep the battery fully charged without overcharging. This also eliminates any danger of acid damage to the bike.
Store the bike where it will be DRY all the time. Many northern garages go through periods when the humidity is 100%. Happens when warm southern winds penetrate a garage where the floor is still frozen and cold. This can result in lots of moisture, rust and corrosion on the poor bike. Even a little heat in the garage will help prevent this. Worst is a dirt or gravel floor since they give off lots of humidity. Better is an insulated concrete floor with even a little bit of heat. Ideal is a dry heated concrete floor, even if it's only kept a few degrees warmer than the outside.
Make sure the bike is protected from direct sunlight, to avoid fading of paint, instruments and damage to seat and other plastic parts. Not as big a problem as summer sun, but no sense in aging things while they are just sitting.
Some people worry about tires and flat spotting, but I have never had this happen, I think bikes are too light.
Last and most important, is to keep the bike where it is easily accessible, you never know when a warm day will come along next spring, and you don't want to miss a chance to ride !!!
