I read through some of the comments on this list about lithium-ion batteries and have a few things to add.
Lithium-ion batteries require *very* tight control of the charging voltage. If you let it go too high, metallic lithium can be produced inside the cell with disastrous results.
The expected lifetime of a li-ion battery depends on more than the number of cycles and the depth of discharge. Unlike Ni- or Pb-based batteries, li-ion batteries degrade significantly even when unused. The rate depends on state of charge and temperature, with high states of charge and high temperatures being the worst.
You may have noticed that while NiCd and NiMH batteries arrive from the factory fully discharged, li-ion batteries usually arrive at 40-50%. This is the level at which degradation is the slowest. This means we should probably design our li-ion battery management algorithms to keep them half full rather than completely full. We can still use the extra capacity to get through an eclipse season, but when the extra capacity is not needed the batteries should not be kept at 100%.
Like all batteries, li-ion batteries are better cold than hot. Since they perform fairly well when cold, some thought should be given to a spacecraft thermal design to keep them cold.
--Phil