There was a thread like this just recently that had a lot of good suggestions. You might want to try and search for it.

Otherwise, wash your hands often, and use eye drops and nasal spray to keep from drying out preventing the need to rub those areas and introduce germs. I was also just on a flight where all the FAs had those air purifier things that places such as Sharper Image and Brookstone sell. I overheard a passenger ask one how well they worked and the FA said it appeared to dramatically reduce the number of colds he got after flying. (Perhaps this had a placebo effect on this FA. There's a thread now on these things where the concensus is that these couldn't possibly work. http://www.flyertalk.com/forum/showthread.php?t=385197 )