Gonna post my thoughts on what OP said.
New Negative Syndromes
Insanity effects- Makes sense, theres deceases that cause euphoria before death, we can have many different mental effects.
Cough up *material* - Sounds nice, should be slightly limited, we don't want dwarfs coughing up magma, and suddenly setting the booze stockpile a flame.... or do we?
Infect Blood- Almost a must have. It's incredibly realistic, and works with the contagious deceases. It would make even plague survivors still a potential threat, and I also think, things like future children and spouses, should also have a chance to suffer from the syndrome.
Faction Change- More on this in a second
Mutation- More on this in a second
Transformation- This, is very similar to faction change, and mutation. If you don't see where I'm going, combining all three we can create things such as werewolves, werebears, vampires, zombies. All potential awesome Fun creaters, and amazing for modding, can you just imagine a fort, constantly at siege by the legions of the the undead, where every dwarf that dies, rises to fight against you? I can, and it's awesome.
Drain Physical Stats- I think this is already in it? I dont know, I think there might at least be the potential in the current frame work. Make it go both ways as well, something makes your dwarf go brain dead, and also make them massively strong.
Alter Temperature- possibly. This could be common with almost all syndromes, like fevers, which could be an early indication, that a dwarf is about to suddenly explode into a swarm of demon rats. And burning limbs could be fine, though this does already happen with normal poisons doesn't it? Theres not much difference from a molten heart, and a heart thats stopped from poison, as far as gameplay goes.
Positive Syndromes
Healing Effects-With every negative thing, they should be at least some positive, have to maintain balance. So this could be especially useful, when magic and alchemy get used.
Cheering Effects- Just look at insanity effects
Curing Effects- I think you're suggestion something along the lines of, syndrome A melts dwarfs eyes, Urist McBadass, survives unharmed, instead of becoming a boon, with infectious blood, his immunity would be granted to children, as well as people dosed in it. This I agree with, makes sense.
Resistance Effects- Works for me. Fits with curing effects, though less extreme.
Raise Physical Stats- Already discussed
Induce Mood- I'd say this is less syndrome related, and more, inspiration from becoming a champion. And the artifact should be predetermined once the creature what created. Or this could just be part of insanity effect.
Syndrome Mechanics
Extract Blood- Should be added, we already have extract from creature in the butchers shop.
Poison Weapons/Traps- Give it a chance to hurt both, alchemist, and soldier, lower with higher skill.
Tonics- Would probably come with alchemy/magic again
Antibodies- Basically the same as above, and yes makes sense.
Divided Classifications: I dont think this is needed. If give the right raw tags, we could be able to do this, and he could just not make things that disobey the classifications, but I don't think they should be required. I would love a poison, that spreads through a dwarfs, blood add cough up blood, and have him cough while constructing the well, only to have an empty fort within the year.
Syndromes the Effect Plants- I love this. This realistically kills thousands all the time.
Plagues- I think these will naturally come out with the development of the system. Be careful of that sickly elf in the back of the caravan, that keeps coughing, but hey, you deserve it for trading with elves I guess.
Plauge Pits- It would make sense to have some special stockpile for refuse that will cause decease. Also we should probably have pyres. Maybe as a constructible building, thats only made of wood, and one time use, unless you used magma.