I was a soldier for 8 years and spent most of my time out of Ft. Bragg hanging out with guys who have absolutely nothing left to prove.
[Sidenote: there are an amazing number of RPG geeks in Special Forces].
One of the toughest, most unflappable men I knew was a senior sergeant I'll call Robert. Now, Rob bench pressed small cars, could run 2 miles in less than 9 minutes, was one of the most experienced jumpmasters on Ft. Bragg, and knew enough martial arts to be asked to be in a Van Damme movie. He was the Real Deal.
In Desert Shield/Storm I finally saw fear in his eyes, though. Real fear. What was the phrase that scared one of the toughest men in the Army?
"The local that's been delivering food might have typhus"
Disease has killed more soldiers than bullets ever will. Parasites are close behind. Indeed, some anthropologists believe that malaria has killed more people than any other single cause ever. That is a pretty big deal. Disease is part of warfare, too, with diseased animals being used as part of sieges for millennia.
What does this have to do with gaming? Well, to me, tons.
That is because disease and parasites can be used like any other threat to drive the plot and give the players a challenge to overcome. Also, they offer a unique opportunity to threaten players regardless of level! A 17th level Cleric with malaria is in about as much trouble as a peasant with the same. Oh, sure, spells can cure it but is the cleric in any condition to cast it on himself when in the throes of a flare up? The characters might not fear a group of Kobolds in their lair, but the sight of roaches scuttling among the piles of garbage and waste scattered throughout could give them pause; after all, the bloody flux doesn't care about your armor class.
No, I don't think you should reduce your players to germ-phobic paranoiacs nor must you plunge your campaign into a grim nightmare of plague pyres and chants of 'bring out your dead'. But just like food and water, concerns about disease shouldn't be absent from your campaign, either. Plus, disease can be a plot point.
Brother Dorn walked slowly down the lane toward the Jonmy home, hoping that the youngest child hadn't taken a turn for the worst. He was too tired to walk any faster, having just come from the Ulrin family home and his attempts to comfort Alsee after the death of her husband.
It was so very odd! Sure, Winter was the time of cold and sniffles, but a plague like this? It was worse than his own youth when the Yellow Death had come. He'd asked the Bishop for aid, but the note back said that every village in the diocese had the Winter Plague and that the senior clerics and even the paladin Sir Eirik were going village to village in an attempt to stop the illness. And that was odd, too, a sickness in every village, even the ones away from the King's road.
Speaking of odd, who was at the well? Even with the plague the women filled their casks during the day, not in the bitter cold of a mid-Winter night. As Dorn came came to the edge of the village square he realized the figure in the middle of it was too tall to be any of the village women. And dressed in a hooded robe?
Then Dorn's sleep-deprived brain realized something that made him even colder than the chill east wind - the figure was pouring something into the well. And the hooded robe might be the dirty yellow worn only by the priests of the Rotted One. But the Plague Priests had been wiped out generations ago!
As he stood there, stunned, the figure at the well, perhaps sensing Dorn's gaze, shot a look in the direction of the religious brother. The two of them spent a moment staring into each other's eyes across the dozen yards separating them, the Brother's face pale in exhaustion and shock, the figure's face covered in a stained linen mask. The moment was broken as the Plague Priest turned to run and Dorn opened his mouth to shout an alarm.
All this being said, there are three elements of my campaign I am including in Far Realms; the Religious Brother and the Healer. The first are custom rulles on diseases and parasites.
The second is the Religious Bother (or Sister) is a non-adventuring (i.e., NPC-only) sub-class of the Cleric. Compared to Clerics, Religious Brothers have fewer hit points, fewer weapon proficiencies, lesser fighting skills, and fewer spells. However, they do serve an important role in the campaign. Where Clerics are meant to represent the Crusading Priest the Religious Brothers (and Sisters) are the village/parish priests, the ordained monks, the fully-vowed nuns, and the other non-combat clerical spell casters. The can be henchmen to player characters and can also be among the followers attracted by high-level Clerics when they build a stronghold.
The third are healers. Healers are hirelings proficient in herbs, poultices, and tending the sick. They can reduce the likelihood of characters getting ill and speed recovery from disease and parasites. In extreme cases they can even reverse the effects of level drains!
Together these three elements allow you both make disease and parasite a motivator, add depth to your campaign with NPCs, and make henchmen/hirelings an integral part of play.