When I was younger, I'd get really sick when we got back from WDW. That happened in 93 & 96. 98, 99, and 2001 (and this year) I was fine during and after. 2003-- nightmare! I got a horrible cold smack in the middle of the trip and had to physically drag myself all over Epcot, Sea World, MGM, AK, and MK. I actually got sick while at Epcot... out of nowhere my throat started killing me, and by the time I had dinner at Chefs de France I was ready to pass out in my french onion soup!

On the way back to POR from Epcot, my throat magically stopped hurting... but suddenly my head and nose were both completely stuffed up, resulting in about 5 million horrible headaches.

The smart thing to do would've been to stay at the hotel, but I couldn't prolong my stay... I was on spring break and classes started again the next week, and at the time I thought I might not get back to Disney for another 4 years or so. If you do get sick and feel like you have to go everywhere, just go slower, don't expect to do everything, take plenty of breaks, drink a lot of fluids, and, possibly most importantly, remember that Tylenol or Aspirin is your friend!
As for avoiding getting sick in the first place, there's not much you can do with germs floating around in the air (other than if you see someone hacking and or having a sneezing fit around you, don't get too close if you can help it; then again "getting too close" to people is kinda inevitable at WDW). Now, if it's caused by touching things other people have handled in shops and the rides and railings, etc., obvious thing is wash your hands. Maybe I'm a little too paranoid, but when I buy something, I never buy (or handle, if I can help it) the thing in the front, I always go behind the front item (although that's also because I want to get stuff that's not smudged and/or knicked up). My other thing is if I, for some reason, don't get a chance to wash my hands before I eat and I'm eating "finger food" I use the plastic forks/knives or just don't eat the part of the food I touch. May sound silly, but I rarely get sick, so my mind tells me that helps protect me, LOL.
