I took off my run-flats and R98 wheels about 4 months ago and put them in my workshop. I stacked them on top of each other under the end of a work bench, so the are not in direct sunlight and are setting where they shouldn't develop a flat spot.

My question is, how often should I put them back on the car and run them in order to keep them from "going bad"?

 

They are going bad as we speak.

Time alone will age your tires.
UV light (direct sunlight) is bad
Heat is bad (cool and dry is better)
Avoid placing tires near electric motors that generate ozone.
Oil or solvents on the rubber are bad.

Make sure they have some air in them and they are covered with a plastic bag and sealed to minimize air/moisture.

See
http://www.tirerack.com/tires/tirete....jsp?techid=37

They might last a year or two in storage but the rubber won't be the same as new. Hard old rubber doesn't grip well and tends to be noisy on the road.