The official campaign (OC) for Neverwinter Nights was based on a disease plague and subsequent city lock-down. I have a feeling it will be quite some time before anyone tries a story like that again.
For the game, usually disease manifests as a reduction in ability scores like strength or constitution. I wonder if that could be extended to include loss of use for equipment slots as well? If you get hit with rot grubs in one arm, for example, you could lose your ability to equip a shield or off-hand weapon. If you have an ear infection, you might not be able to wear a helmet. If you get a foot fungus, then you can't wear magic boots.
