(1) I am waiting for John.

(John is not here.  I am expecting John to be here soon.)

(2) I am waiting on John.

(John is here.  I am serving John.  If he wants tea, I take him a cup of tea.  If he wants toast, I take him toast.  I am probably a waiter or food server.  I am probably NOT a friend of John's.  Or perhaps I am saying "wait on" to express sarcasm or criticism.) 

(3a) I am waiting on John.

(John is here.  John is doing something, and I am waiting for him to finish doing it so I can do something else with John.)

(3b) I am waiting for my Aunt Belle to finish her lunch so I can take her to the library.   (I am waiting for her to finish one activity before beginning another activity with her.) 

GOOGLE will give you many examples of "to wait on".  Its use seems to change in some regions.  I am from the Pacific Coast, and the above examples sound fine to me.  I do not picture myself saying, "I will wait on Mary at the corner."  I would say, however, "I will wait for Mary at the corner."  The difference is subtle but it exists.