Do allergies run in your or his dad's family? My kids are allergic to tree & grass pollens, but fall is just as bad on them because of all the leaves falling (some pollens stick to the leaves and when they dry up they cause my kids issues). Some kids will only get a runny nose & get congested, but others will get the red, watering and puffy eyes or a cough also. Sometimes it is hard to tell if it is just a cold or allergies. Personnaly, if I don't treat the allergies (Zertec - 2 of the 3 were on it before they were a year, the 4 yr old was just started this year he isn't as bad as the others 2 though) mine will end up needing treatments for ashma... or when it gets to bad I can't treat at home - off to the hospital we head and hope it's not another hospital stay (cause thouse are never less the 3 days).
Might want to check into the family histories a little or talk to a doctor and see if he does have allergies. They are something they can "grow" out of, but please don't let him suffer through them.
Oh, and humidifers aren't always the answer... when my daughter was in the hospital - I was told they are one of the biggest NO NO's for kids with allergies and ashma. Because they actualy can cause the airways to restrick more - which means it is even harder for the little guys to breath and keep their O2 levels correct.
Good luck & I hope his runny nose clears up soon!