Intergalactic disease among humans

[Dangerious P. Cats]

I've been watching through Stargate Atlantis and something struck me about encountering humans separated by thousands of years on other planets with different eco systems is that you'd get different diseases evolving among different populations and likewise people in different populations not having any immunity to diseases brought by interplanetary visitors.

So how might the same species living on different planets apart for thousands of years affect the development of viruses and bacteria? And what kind interesting roleplaying scenarios could this lead to?