I'm interested in the replies to this thread too! For our 4-year anniversary, my boyfriend got me a fabulous little gal from our local humane society. We fell absolutely in love with her, and she ended up having (we think) FIP. We had to have her put to sleep, and my heart is still broken. Our two current lovely little monsters were adopted from a different humane society, and they have (we think) feline herpes. Now, the feline herpes is not so bad to deal with...the eye infections were pretty chronic when they were very small, but we've had none in a while now (knock on wood!!!!).
Given our 100% rate of infection with feline viruses, 1 being horrific and fatal, my boyfriend and I were wondering if just having so many animals in the humane societies was just setting us and kitties up for disaster, or if we were just unlucky. Both facilities looked clean; of course you can't see microbes, but I did look for blatant overcrowding, unclean litterboxes, etc.
Next time, we might just go the paper route. Not to say any old kitty out of the paper can't have any host of diseases either. Maybe we're just meant to be caregivers to special kitties, but that's a hard lot in life.