Farmers and fishers, if they survive to old age, often develop a type of white skin cancer (uh... I think the medical term is "actinic keratinosis"), on the exposed parts of their skin (face, ears, hands). My grandfather had to have an ear amputated because of that.
There are other types of these 'cancer clusters' related to some professions:
http://en.wikipedia.org/wiki/Cancer_cluster
I agree with the writer's callous. I've got a rough bump on the left side of the tip of my middle finger of the right hand, from school. Even though it's been nearly a decade since I wrote much by hand, it's still there.
You might also consider scars for cooks (splashes from hot fat, thin white lines where a cut from a sharp knife healed).
A (Al-)chemist or apothecary might have discolorations or stains on his hands. Weighing out small amounts of potassium permanganate ("Condy's crystals"; used to make disinfectant solutions and, at least today in Germany, illegal to sell in large amounts without special reasons) leaves brown stains on your skin. Nitric acid reacts with the keratin in the skin to cause yellow stains, which will peel off a few days later. (It doesn't hurt. When I was in the early parts of studying biochemistry, watching people peel of the dead skin patches during lectures was the way you could always tell who was doing their first year inorganic chemistry course.) Today nitric acid is mostly used to create fertilisers or explosives, but pre-industrialisation, aqua regia would have been used by alchemists and maybe people working with gold (miners, jewelers, artists). Alchmists also used "aqua fortis", which is nitric acid in water.
If you want to know more about the physical results of being an apothecary or chemist, I can ask my mother about it. (She's a 3rd generation pharmacist and interested in the medieval origins of the profession.)
ETA: You might also consider the nutrient supply people from different social strata or regions had access to. For example, a miner or a mountain farmer would be much more likely to develop goiter than someone living near the coast with access to a regular supply of fish and seafood. This is also dependant on the soil. A lot of elderly women here in Eastern Germany had to have their thyroid gland removed because it developed suspicious hot nodules, which is linked to our soil (and therefore the bread and vegetables) containing very little iodine.
Wikipedia tells me the Crusaders often suffered from scurvy. And even though the use of citrus to cure it was known by Vasco da Gama's time, millions of sailors still died of it before the beginning of the industrial era.