I've had the same problems, now there are a few things that are mandatory for each trip. I'm travelling 2-3 times a week on planes and unless you beef the immune system up, your going to get sick.
1 - Take Airborne
This works really well, you can get "Airborne On The Go" at places like Target.
Just pour the packets in to water and glug it down about 1/2 hour before getting on a flight.
2 - Carry Zicam
I am not really someone who takes medicine or pills. However, 3-4 years ago my wife introduced me to Zicam. She told me it was "herbal" and I looked at her with that "yeah right, this is really going to work" look. As soon as you feel a sore throat or a sniffle, get one of the tablets or one of the chews inside you and it will either prevent a cold or will shorten the duration. I always have these in my briefcase when travelling.
3 - Wipes
Like other people said, you have to have these on planes for wiping down the tray, the armrests, even the TV screen and definitely for when you get up and use the bathroom.
The other thing I always do is make sure that the plane air vent is turned off or pointing away from me. Who knows what germs are being circulated by that thing.