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I have a lot of Eneloop batteries and am very happy with them. However, many of my devices, annoyingly take an odd number of batteries, but the Eneloop charger only charges in pairs.
How bad is it exactly to charge two batteries together that are discharged to different levels? How bad is it to charge two batteries together that are not even the same age or model?
If your charger literally must have a pair of slots occupied to charge then you should probably retire it. This suggests that it probably (not certainly) charges the pair in series. If this is the case then significant reduction in battery lifetime can occur OR one battery may be grossly undercharged, depending on the charger end point decision method. Chargers that work in that manner are usually old and or cheap (and if not cheap, should be). Eneloop batteries are excellent products with long cycle lifetimes and low self discharge and deserve to be treated well.
I'd recommend a decent charger. Look at the candlepower forum pages for ideas on what is good and good value. I uses a "Maha", "Wizard one" charger and find it excellent. They are dearer than some alternatives. You'll never regret owning one once you forget how much you paid for it :-).
The cardinal rule with charging NiMh batteries is to get a charger that has an independent charging circuit for each battery. Do not assume that the charger that came with the batteries is a good one. It probably isn't.
MaHa has a series of reasonably priced chargers that charge each battery independently. You want a pulse charger that measures the voltage of each cell independently and turns off the juice to each cell when it is fully charged. This will make a HUGE difference in the lifespan of your batteries.
If you don't use such a charger then you risk over-charging and damaging some of your cells, or in the best case, under-charging the other cells in the charger if the charger happens to measure a cell that is more charged than the others. Over-charging is very bad for NiMh cells.
The real answer to this is answered by a question "just because there are spots for two batteries - why must you fill them both?"
There is some variability allowed in parallel charging simply because every battery is different (slightly) and even if they come form the same device they will discharge slightly differently. If you are concerned about a major difference in discharge, simply charge them one at a time, leaving one spot open.
