Actually, in the case of Li-ion and Li-polymer batteries, they are better being kept topped-up all the time, if you deep discharge them they will lose capacity over time - here's a bit from a Compaq white paper on iPaq handheld batteries.
"If the iPAQ will not be used for 2 weeks or more, and will not be connected to AC power during
that time, Compaq recommends backing up your data and applications and moving the battery
switch to the OFF position. Leaving the battery switch in the ON position for longer periods,
without keeping the iPAQ connected to AC power, can eventually damage the battery, reducing
its capacity to hold a charge."
If you're interested, the whole document is available here:
Battery white paper