You should tell your users to unplug their Macbooks more often. If you leave them plugged in 99% of the time the battery will fail a lot faster. It should drain and recharge every once a while.
At this point, this should be a configurable option in the hardware and system software. Configurable, so that if you want to use it, you can tell it when. (E.g. I work from home on Sundays, so run from battery down to n percent charge before switching on recharging. And/or alert me when I exceed the recommended runtime between charging cycles. Etc.)
I suspect, however, that the cost/benefit -- from the manufacturers' perspective -- for implementing this is not favorable.
I can't find any reference anywhere that what you say is true, can you point me in the right direction please? As far as I know, the complete opposite is true for the Li-ion batteries that Apple uses, each discharge reduces its life.
Cadmium batteries have a memory effect and need to be drained every once in a while but Apple doesn't use those.
While each full charge cycle reduces the overall life, Apple recommend going through at least one charge cycle a month: http://www.apple.com/batteries/
This isn't the same as 'run it down to 0% and then fully charge', though, it could be 'run it down to 75% and then fully charge, four times'.
