Something new that my sons' pediatrician recommends for coughs is corn syrup. Medical professionals are realizing that most cough/cold remedies actually do no good for kids. Corn syrup is actually an old remedy and you give about 1/2 to 1 tsp to help control his cough (better than any of the commercial cough syrups) and also it really helps soothe a sore throat. Plus it is soooo sweet that you'll have no problem getting him to take the "medicine", and it is inexpensive. For my baby I dilute it in warm water (to give through a bottle) as warm water is also excellent for upper respiratory problems, as well as cough/sore throat. Make the water as warm as your son will allow it to be. You are right on to give him warm water with honey!
As far as a humidifier goes, it is an excellent idea to use one but I would use cool mist rather than warm as it will resist breeding the germs a little better. Another less expensive option is simply getting the bathroom all steamy and having your son stay in there. Either in a nice, warm bath or even just hanging out in there (just stay with him, of course!). Turn the shower on hot and shut the bathroom door. Even bundle the kids up and take them outside once it stops raining. The cold, wet air can do wonders.
The average virus takes something like 7-10 days to run its course. If your son isn't better, or seems to be getting worse, in that time period then he may need prescription medication.
I will send healthy thoughts your way :o)