Li-ion tech is a major pain in my ass. Storing them discharged damages them. Storing them charged damages them. Keeping them topped off damages them. Fully discharging them damages them but your battery might have a protection circuit so don't worry about it. But it might not so worry about it. You've apparently got to store them half-charged for optimal lifetime but there is a lot of wrong information out there.
I think I want to power my devices with disposables, thanks :-)
Since I am no expert in chemistry, I rather point to an article here: http://batteryuniversity.com/learn/article/how_to_prolong_li...
Basically, the capacity degrades over charge/discharge cycles. The reason is pretty simple to explain, because you can't really operate the batteries in perfect condition, it always get worse while discharging and charging it.
The other conclusion of that report points to the fact that depth of discharge is related too. So instead of using it from 100% to 0% (actually 0% doesn't mean nothing left, it just means the phone can't operate on that voltage), recharge as soon as you have a plug.