I tend to give commendations after loot, and mainly to players that I notice do some part more right then average and/or communicate well.

Was the limit break used well, or not? So many times I see it not used at all.
Was the Tank positioning the mobs in a way that benefits the type of dps we have? Matters less with casters and bards.
Are they still in the instance? Can't commend someone who has instantly left.