Li-Ion cells should be charged before they run down to empty. You can top them up as often as you like, even if you have only used them for a few minutes.
Here is a useful table illustrating Li-Ion cell capacity, which has been reproduced here several times:
4.2 volts 100%
4.1 about 90%
4.0 about 80%
3.9 about 60%
3.8 about 40%
3.7 about 20%
3.6 empty for practical purposes
<3.5 = over-discharged
If you do discharge them to empty, the quicker they are put back on the charger the better.
Don't store Li-ion cells either 100% full or empty (although empty is worse). The best long-term storage voltage for them is ~50% (3.8V-3.9V)