Taken from an informative post by by forum member GMK:
I have a feeling that much of what's being discussed re: deep cycling the BB Li-Ion batteries is really more suitable for Ni-Cads.
It is my understanding that Li-Ion batteries benefit little and in fact it can be detrimental to initially, never the less, often fully drain and recharge them to condition them. With Ni-Cads, this was certainly the SOP, and battery life was very dependent on the deep cycle routine. Many electronic devices, such as notebook PCs had deep cycle routines built into them to re-condition their Ni-Cads.
I haven't seen anywhere wherein RIM recommends deep or discharge cycling but I have seen a number sources where the care of LI-Ion batteries is best served by keeping them topped up.
There are plenty of sources on the Net on the subject of battery care. Here's a couple: How to prolong lithium-based batteries http://en.wikipedia.org/wiki/Lithium_ion_battery
To save some time a couple of quotes:
"# Unlike NiCad batteries or NiMH batteries, lithium-ion batteries should be charged early and often. However, if they are not used for a longer time, they should be brought to a charge level of around 40%. Never use the battery care functions some cellular phones provide for nickel based batteries. (This will deep cycle the batteries.)
# Li-ion batteries should be kept cool. Ideally they are stored in a refrigerator. However, they should not be subjected to freezing temperatures. Aging will take its toll much faster at high temperatures. Keeping them in burning hot cars can kill lithium-ion batteries.
# Buy Li-ion batteries only when needed. Look at the manufacturing date. That is when the aging process commenced.
# When using a notebook computer running from fixed line power over extended periods, it is advisable to remove the battery and store it in a cool place."
From Battery U. (Actually CADEX Electronics)
"A lithium-ion battery provides 300-500 discharge/charge cycles. The battery prefers a partial rather than a full discharge. Frequent full discharges should be avoided when possible. Instead, charge the battery more often or use a larger battery. There is no concern of memory when applying unscheduled charges."