Most Energy Efficient Charger Design?
Although multi-chemistry charge solutions exist (typical device linked), they each have their own charge sequence requirements and charge power.

Some useful links:

Charging Lithium Ion, Charging NiMH, Charging Lead-Acid. 

There are numerous articles available on each type. My point here is to support the other answer that each charge type should have its own port as you can usually only use the charge controller in one chemistry mode for a given design as it is nigh on impossible to detect precisely what you have just attached.

Note that multi-cell stacks may need cell balancing for many reasons, including safety.

HTH