Lots of great ideas so far - I will agree with many and maybe throw out another idea.
First off, I agree to really stay on top of your son's fever. That's a sure sign that your little one is fighting something, and should not be overlooked.
The saline drops in their noses and aspirating the mucus from baby's nose is a good place to start with helping him to breathe better. Humidifiers are great, especially if you're in a dry climate.
One thing we have found to be SO helpful are the Sudafed Plug Ins. They give off a Vicks-like vapor and is not medicine that is ever ingested. All three of my daughters have had great success with these, and it has helped them to sleep. I would try that!
Another strange thing I have found is to put Infant Vicks rub on the bottom of baby's feet. Then cover feet with socks or footy-pj's. It sounds crazy, but I have had a LOT of people tell me that it helps with coughing and breathing as well.
It's so tough, and you hate to see your family have such a tough time. Wash hands all the time!
Hang in there - hopefully it will pass soon enough. Can't promise, but hope some of these ideas work for you. Always talk to your pediatrician if you have any questions about anything - they are used to parents having lots of questions, and you'll feel better checking in with them as a mom.