Hello all,
It is appropriate that I am writing this since I performed most of the steps I am about to mention. Feel free to critique or recommend something to my methods so that I may edit this guide. I am referring to 6-12 month storage and have performed the following steps.
1.) Lift the bike off of the ground (especially cement). Tires will develop a flat spot over time and the condensation from concrete may speed up tire deterioration leading to dry rot. If you don't have stands, place a vapor barrier (plastic) on the concrete and then add some carpet to minimally cushion the tire.
2.) Pour some Marvel Mystery Oil and Sta-bil in the tank (should be near empty). This will ensure that the top of the cylinder gets some lube. If you have time, it is preferred to remove the spark plug and pour 10-15cc of oil to prevent rust/oxidation. This can be a pain on in-line 4 motors and very time consuming. I just poured MMO into the tank and ran it for 15 min (1/4 fuel).
3.) After the bike cooled down a bit, I removed the oil drain plug to change the oil. Warm oil drains faster and more efficient than cold oil. I replaced the filter to ensure minimal contaminants remained in the engine. It is important to change the oil before you store since used/burnt up oil becomes more acidic and can speed up the damage to engine internals when left concentrated for a while.
4.) Replace oil and use Marvel Mystery Oil for the last quart. Top the engine off with fuel and add the appropriate amount of Sta-bil. Expose the throttle body and/or carb intake and spray Sea Foam (Deep Creep) while the engine is running to fog the engine. *If you have a carbureted bike turn the petcock off and wait until the bike shuts off. Drain the carb bowl to ensure the carb is free of fuel but has been coated with Sea Foam and the Marvel Mystery Oil combo.
5.) Stage the bike and remove the battery (if it has one). Put the battery on a trickle charger such as a Battery Tender to keep the battery fresh.
6.) Cover the Bike (even if in the garage). Never use a tarp since a tarp retains moisture and keeps it close to the bike causing oxidation. Motorcycle covers or even porous cloths are preferred since they block moisture from the top but let moisture underneath to evaporate.
**Some motorcycle shops offer storage programs that ensure your motorcycle gets a monthly review an stays fresh until your return.**
IMO you are better off leaving it with a full tank of fuel that doesn't contain ethanol, but still with the stabil in it.
By doing so you will stop air and water from getting to the inside surface of the tank thereby preventing it from corroding.
You don't want to use a fuel containing ethanol though as the stuff is hygroscopic and will suck moisture out of the atmosphere which will cause rust to occur.
So essentially do as Havoc has said above then when you have the bike laid up fill the tank to the top with new fuel that has already had stabil mixed into it.