It sounds like the cat colony has an upper respiratory virus that is being passed around. You can read about these diseases here
http://www.marvistavet.com/html/feline_upper_respiratory.html
Sharing dishes and being in close proximity to other sick cats will pass such diseases around.
For your own cats keeping them as inside pets with no access to the strays may be safest though of course vaccination will reduce risks of getting infections.
Feline aids is contagious too
http://www.sniksnak.com/cathealth/fiv.html
Unfortunately for viral infections there is not a lot that can be done other than vaccination or treatment of symptoms.
Hope this helps you!
Cat Health, Behavior, Care Expert
30+ years cat owner, rescue, breeding, study of behavior & health care
You are welcome and thanks for the above accept.
You might want to work with a group that could help rehome some of the younger or friendlier ones. Check out the cat rescue groups in your area on www.petfinder.com or go to the local pet section on www.craigslist.org and ask about local cat rescue groups.
I'll close out this question now.