LiIon lifetimes are typified by total number of complete discharge/recharge cycles. That is, if the battery is rated for 1000 cycles, then doing 2000 half-discharge/re-charge cycles is approximately the same (I'm really stretching things here, but in the largest sense, it's mostly true).
So, it really doesn't hurt the lifetime of the batteries by only partially discharging them before re-charging. It seems that the only thing that can hurt them is to run them down flat, then leave them for long periods in storage (aside from subjecting them to defective chargers, or short-circuiting them -- but then you might not live to tell the tale). LiIons don't self-disharge as quickly as other battery chemistries, but they are meant for active users, like cell phones, MP3 players, Gameboy Advance SP, and the like. If you use a LiIon-driven package only once every six months, you might find that the battery will no longer accept a charge when you go to use it. That is usually due to a safety circuit in the battery package that disconnects the cells to prevent dangerous chemical reactions. It's actually dangerous to run a LiIon cell too flat, and there are safety electronics in the packages to prevent this from happening, especially to prevent you from attempting to recharge a cell in that condition.
Also, because a lot of electronics will pull a miniscule amount of current from the battery when switched off, if you do intend to not use a unit for a few weeks, it's a good idea to remove the battery. I have a Canon camcorder that behaves this way. If I leave the battery on the unit, it will run it down in a matter of days. If I remove the battery, it will still have a reasonable charge on it when I go to use it a few weeks later.
The most annoying thing about LiIon's and the reason you don't seem them used in more applications, is that they have a per-cell voltage of 3.6V. This means that they don't easily replace the more common 1.2V to 1.5V cells you normally encounter. The circuit has to be essentially redesigned to run off of multiples of 3.6V cells (3.6, 7.2, etc.) instead of multiples of 1.5V (1.5, 3.0, 4.5, etc.)