Hi! :)
I absolutely hated to see my babies that way so I feel for both of you! :(
One of the things I would do was to make sure that they were always in a sitting up position so that the stuffiness wouldn't make them gag/choke. They sell Baby Vicks that also helps if you apply it to your babies chest, back and neck area. Some go as far as putting a bit on the babies upper lip or nostrils but that can actually cause some discomfort so be careful of that. Or do what my grandma would do and wipe some on a kleenex and then put that kleenex with the Vicks inside your baby's shirt. This way they inhale the good stuff but don't have to have skin contact with it at all.
They also have saline drops but if you're brave enough to try those more power to you. My kids would scream their heads off and I hated holding them down to do it so I never tried more than once.
Other than the humidifier which you are already doing, I don't know of any others beside medication. If push comes to shove infant cold drops at the pharmacy are wonderful. They will help you and him get the much needed rest and you will both feel a whole lot better!
Good luck and have a great weekend! :)
M.