Some interesting information about rechargeable Lithium Ion batteries at Wikipedia:
http://en.wikipedia.org/wiki/Lithium..._and_discharge
I let my batter get down to around 15% and then charge up. I have no idea if this helps or hurts or doesn't matter. In general, I believe that it doesn't matter... someone more schooled in the art of battery technology (which does consist of some gray area, to be fair) may know (or think they know) better.