As far as I know the common influenza or common flu comes from pigs, if I am not mistaken.As for many other common diseases that humans face.
They come from farm animals, because people have always been close and around animals like cows, pigs, chickens and so on. That's why when the europeans first came to the americas millions of native americans died of measels and small pox and things like that. Native americans did not farm and were not immune to european diseases that they got from farm animals.