S.D.
I've travelled w/ healthy kids and have have to travel home when they've had ear infections (as a 1 and 3 year old) ... I would say .. other than the obvious drinking/sucking thing during the flight ... be sure to have all your necessities handy ... also, while you might not normally do this ... we usually end up doing lots of snacking on the plane .... if it helps the trip move along - then one day with extra snacks certainly won't hurt them. :-) So, pack lots of food goodies. :-)
Lastly, if you find that you think he may be uncomfortable, I'd give him some tylenol before the trip - just to cover any aches/pains just in case - again, that just MY opinion.
S. :-D