Wow, that was a big necropost. The last post was 2-1/2 years ago.
Don't deep-cycle Li-ion batteries, this will shorten their life. Li-ion does not develop memory the way NiCd does.
For modern high-capacity lithium-cobalt cells such as the Panasonic NCR18650B, the optimal open-circult voltage is about 3.6-3.7 V, which represents an approximately 35-45% state of charge. Avoid discharging batteries to below 2.75 V under load or 3.2 V open-circuit, as this will shorten their life as well. Discharging to less than 2.5 V open-circuit will damage the battery and compromise safety, and attempting to recharge a battery at an extremely low voltage (less than 2.0 V) can result in a fire. I would personally try to avoid discharging below 3.5-3.6 V open-circuit whenever possible for optimal service life.
Today's Li-ion batteries are designed to operate to slightly lower voltages, which expains the lower voltages I'm giving. Cells using older technology generally should not be discharged below 3.0 V under load or 3.6 V open-circuit.
—DragonLord