I've got three bricks in the garage now, and have owned five over the past six years and they have all done nicely on my storage regime.
First, I do all the annual maintenance, splines, brakes, fluids, valves, etc. Then I fill the tanks with no-corn mixed with Stabil and Techron.
I'll apply a light coat of a corrosion protectent concentrating on the lower parts of the bike being careful not to get any on the brake rotors, I use the stuff from S100. This helps protect them from the puddles of saltwater that drips off the wife's car. I cover them with those lightweight $20 motorcycle covers I get on ebay to keep dust off.
Every couple weeks during the winter I'll go out and start them up, letting them run at fast idle with the transmission in first or second gear until the engine gets warm enough to cycle the fan. This charges the battery, gets rid of the condensation in the crankcase oil, and circulates the oil in the transmission and final drive.
I got a couple cheap $15 K bike trickle chargers on ebay that I'll plug in once in a while to see how the batteries are doing. They have an LED that goes from red to green when the battery is charged. I connect the charger to the power outlet above the coils. Usually the LED is green indicating a fully charged battery that isn't low enough to start charging. If I turn on the ignition and headlight, the LED turns red, and if it goes back to green in less than an hour or so, I am pretty sure the battery is fully charged, which means the battery is holding it's charge.
Last, and this may be a sign of a serious neurosis, but I check tire pressures once a month, and rotate the front tire a quarter turn to avoid having the weight on the same spot all winter. The first year I had my K75RT it sat for four months on a soft tire which made a flat spot that took a couple hundred miles to get rid of.