Best way to use sets of 4 rechargable batteries with appliances that need only 2 or three?
NiMH batteries are much more tolerant of partial discharge/recharge cycles than the old NiCd ones, so I wouldn't worry about whether or not they are being run flat.

The third rule is the important one.  If you mix dissimilar batteries, then one will always be a bit weaker.  This will be the one that gets run flat quicker, and if left too long, the other batteries may end up pushing a charge through the flat battery.  This recharges it the wrong way, damaging it and making it even weaker next time.

Also beware of batteries that have been left too long after being charged.  Some of the charge will have leaked away, so it will be like using a battery of a lower capacity.  All the batteries in a set should ideally be freshly charged.