This is the peril of preschool and daycare: or any larger group: all those things our little ones didn't get sick with before just jump on them. He's catching up. My son is in a similar situation; he moved from my preschool of 4 kids to a group of 14 daily (20 or so total) and wham! every other week, it's something new coming out of somewhere! We give him a good multi-vitamin, completely eliminate dairy when he's symptomatic, and just try to support his getting well the best we can.
It's a hell of a lot better at three, though, than it was at 6 months or even a year or so ago. They seem to take colds and bugs better than they used to (in my opinion). They're more distractable, which really helps.
The best thing we can do to for the kids is to teach them to wash their hands well, to use tissues, all that. I agree with Jaimee; I see more sick kids in groups where hand sanitizer is frequently used than I do with plain old soap and water. Yvonne is right on, too, about naturopaths; they are wonderful in how they take such good information from us and put it together as a holistic picture. Pediatric chiroracters and cranio-sacral therapists might be able to significantly help, too.
For what it's worth, I spent my first 3 years working at daycares getting sick. It's now rare for me to be down with a cold or flu. So there's a plus!
H.