Just think of "stack" as a "combination". Sometimes supplements (N.O. for example) is most beneficial for a few months before you need to cycle off of it for a period of time. (You do this because your body becomes adjusted to the supplement and therefore less effective after awhile). So to optimize times when you are "on" certain supplements (legal or otherwise) you "stack" certain supplements that are mutually beneficial. However, most of the time for non-steroid usage, the word "stack" will just mean "taking specific supplements at the same time".
This might help: http://www.muscleandfitness.com/nutrition/your-first-supplement-stack
P.S. - Creatine, BCAAs, Omega 3-6-9 are key for me.