Yardbird is the one in this thread with the right info!

I develop power systems for portable electronics. Batteries and Fuel Gauging Algorithms are my specialty. I am an Engineer, and when it comes to batteries, they've given me full control of the train. (I'm even allowed to blow the whistle. (I R AN N-GA-NEER!)

Li-Ion batteries are best stored about 1/2 full. (Or if you're a bit of a pessimist, 1/2 empty.) When full, if the cells are exposed to elevated temperatures, their capacity is permanently reduced. When empty, if they see small load currents for a long time (like the electronics built into most of the packs to protect against overvoltage), their capacity is permanently reduced. So 1/2 full is the preferred storage method. Removing them from the remote will also eliminate any load the remote may pose, and will keep them at 1/2 full.

For NiCd and NiMH cells, it doesn't matter if they start out full or empty. Their self discharge rates at room temperature are over 1.5% per day, after about 60 days, they will be empty! Severly depleting them with a load can cause cell reversal. Certain elements in the cell, change from Anode to Cathode, (and Cathode to Anode) and can cause permanent damage as well. When storing NiCd or NiMH, it is best to remove them from the device to ensure that all load is removed from the cells, and store them in a room temperature environment. Having them exposed to very cold or hot temperatures for long periods reduces their capacity.