For those GMs who use disease in fantasy settings there are several options. For this post, disease is a communicable negative impact on health. So I am excluding real diseases like cancer, beriberi and allergies.

The first thing the GM has to decide is what is a disease? It could be a curse, evil spirit or microbe (or all of them). Spells like Contagion could result in any of these. Spells and magic items that cure or prevent the spread of the disease are type specific. A mask that keeps microbes at bay will have no effect on a curse.

Curses are the result of certain spells, monster powers or side effects of magic items (they are listed as a drawback). Disease as curses means curing may be as simple as casting Remove Curse or Cure Disease. Or it could mean that a cure requires some sort of quest to get a needed material component or to take the ill individual(s) to a specific location. The danger, as with most diseases, is exposure. If the PCs come down with the illness before they can finish the quest, they may very well die. The spells that create communicable diseases as curses should be no less than 7th level, out of the hands of the majority of spellcasters.

I can think of two examples of evil spirits as diseases. Feverman, the first episode of the series Monsters, and a couple monsters in Green Ronin's Shaman Handbook. To cure the ill, one has to destroy the spirit. In many cases this is one on one combat, though for particularly powerful spirits, combating them may involve the whole party. It might even involve more people if the spirit escapes in a community. Spells that can destroy spirits without a need for combat should be spirit HD +6 levels or higher. Or one might use the turning rules, driving spirits off and probably infecting others. Because they are disease spirits, these creatures do reproduce and can infect many after the incubation period has passed...

Microbes as diseases are probably the most common because of how most fantasy settings are based on the real world. But that doesn't mean they have to be realistic or mundane. These microbes are exposed to magic constantly. If magic side effects can mutate larger creatures, they can mutate germs. Some famous diseases are the result of combinations of strains of viruses (swine flu) or the exchange of genetic material between bacteria (MRSA) and if that happens in fantasy settings, diseases may be much more virulent. On the other hand, they are hit with a lot of divine magic that destroys them. In Nyambe this has resulting in resistance- the disease require a skill check to cure (it has been a while since I read it so I don't remember the skill). I do and do not like that. It depends on how I want to view divine magic in a setting (and if the diseases were divine creations themselves). Another result of a lot of use of Cure Disease might be the destruction of deadly diseases, leaving those that are not lethal. People get sick all the time but they don't waste away because as soon as their health deteriorates beyond a certain point, the disease is destroyed. That is a very strong evolutionary pressure. Of course there should be some flare ups, usually the result of places where divine magic is rare or absent (some humanoids like quaggoths or norkers). Once the plague kills its initial hosts, it may spread through the animal or monster population and slam nearby human (and allied) communities. So many people are ill that the clerics simply can not keep up... So in such settings, diseases should be common but cause minor penalties at most.

So keep in mind that you do have options when you decide to plague the characters.