So, for the uninitiated, syndromes are the the things the let the game have the cool new "Poison" effects for blood or breath. They're awesome now. They could be much more so.
There is a sister thread to this in modding,
http://www.bay12forums.com/smf/index.php?topic=61566.0 , to discuss things that can be done with the current system.
Broken this post up by subtype for reasons of length; please comment/submit your own ideas. A lot of these are fodder for modders, so don't worry if they seem too nasty- they wouldn't necessarily be in the vanilla.
New Negative Syndromes
Insanity effects- let there be a poison effect that alters the dwarf's mental state. You could have a rare megabeast whose blood causes your dwarves to tantrum or go berserk, or some sad netherworld creature whose breath causes any dwarf who breathes it to become depressed and waste away.
Cough up *material* - we already have a "cough up blood" syndrome that causes a creature to produce a little bit of blood. Modify this so that instead of creating a little bit of the creature's blood, it creates a little bit of a material determined in the raw files. This is important because it allows for the material coughed up to have a syndrome tag itself- perhaps causing the same thing, and then, voila, you have infection diseases. "Syndrome A causes you to cough up liquid B, which has a contact syndrome tag to cause Syndrome A
Infect Blood- a more realistic/complicated way to introduce infectious syndromes, this one causes the syndrome in question to be applied to the creatures own blood. Example: Urist McCarrier kills a forgotten beast with a nasty blood effect; the blood causes temporary necrosis, which Urist somehow survives, but also permanent infected blood. Six years later, Urist is leading the dwarven army when a lucky goblins nicks his femoral artery, and over the next month half the military succumbs to necrosis.
Faction Change- not useful for much besides zombie plagues, but turns the dwarf to another, syndrome-specified faction. Almost the same as a berserk tag, but won't attack eachother.
Mutation- we have procedural generation, yeah? Can you procedurally mess with something? Make the infected dwarf grow an extra arm, or have his heart on the outside.
Transformation- this one might be tougher to code, but gradually add directed mutations to turn a dwarf into something else. Sheep? Demon? Elf? The only limit is your creativity! (Or decency)
Drain Physical Stats- don't get bitten by the wrong sort of undead; they'll tank your immune system, dull your reflexes and make your muscles atrophy on the spot.
Alter Temperature- changes the target's homeotherm, maybe for specific body parts. Now there's a new magma-dwelling vermin, but this one causes your dwarves' hearts to burn when it bites them
Positive Syndromes
Healing Effects- instead of damaging the organs targeted by the syndrome, it causes them to heal, or even regenerate. Imagine how much more valuable Unicorns would be if their blood caused any champion doused with it to heal nerve damage or regrow lost limbs.
Cheering Effects- the opposite of inducing insanity, some syndromes could cheer the target up, or even have a chance at removing melancholy/berserkness. Would be very difficult to implement in your fortress without work (see "Syndrome Mechanics"), but very valuable- rare, difficult-to-capture creatures could occupy your zoo, and their breath would bring the mad back into society.
Curing Effects- the syndrome that doesn't play well with others. Anyone exposed to it has a % chance of recovering from any other syndrome they're under. Give your doctor a pet *creature*, and let that creature breath on the lepers. Combine that with the "Cough Up *material*" thing and boiling points, and you could have a champion who, after killing a certain megabeast, becomes a savior whose breath cures others of their ills.
Resistance Effects- Cowpox vs. Smallpox. Attach this to a poison with mild negative effects, and it makes the person more resistant to specific other syndromes, or to all syndromes in general.
Raise Physical Stats- Make a very nasty monster with blood that boils at room temperature. As a vapor, whoever breathes it gains strength, speed and dexterity... so whatever champions kill the beast gain its power.
Induce Mood- being marked with the blood of a certain megabeast gives a dwarf incredible inspiration to build an artifact- maybe, if Toady feels like programming it, one related to the death of the megabeast. Would probably need a different mechanism, cause otherwise you could set it up to mood every dwarf in your fortress... maybe only the thing that kills the megabeast, or maybe just ups your chances? For an alternate, have it induce a fell mood.
Syndrome Mechanics
Extract Blood- lets you extract a captured or tamed creature's syndrome-rich blood into a vial, to be used for poison or tonics. Or maybe gather spilled blood off the battlefield.
Poison Weapons/Traps- everyone wants them, and for good reason. Just let the alchemist take a weapon and a vial of negative-syndromed stuff- gnomeblight, the blood of a megabeast, whatever- and make it so that anyone struck with that weapon suffers the effects as if it were a poisoned bite.
Tonics- additional hospital option. Probably. If you have a vial of liquid with a beneficial syndrome, let the hospital use it for appropriate treatments- or maybe just some general option "Apply vial of X to dwarf Y". Would probably be the most difficult to implement, but imagine how much richer the hospital system would be, if you had a whole, carefully-guarded stockpile or gathered or imported cures. You might have some general "Medical Supply" tagged materials- herbs and the like- that doctors of sufficient skill could make custom "Cures" out of.
Antibodies- let dwarves who have already suffered from one syndrome be immune/resistant in the future; probably the only way to implement plagues in the vanilla, cause otherwise dwarves would keep getting re-infected and it would be impossible to scrub it from your fort.
Divided Classifications: Let each syndrome fall under one of a number of types- "Disease," "Poison," "Genetic," "Curse", etc. Each one would be treated in a mildly different way by the game, with different guidelines for moderators- poisons should not be contagious, though a disease that made a dwarf produce poison would be interesting. Dwarves would gain resistance to a disease after being exposed to it, but maybe not to a poison; a genetic syndrome would pass down to offspring. Curse would be uncureable by doctors, but poison and disease would both be potentially treatable.
On-consumption Poison- of limited efficacy, as your dwarves will need to eat the thing in question, and you'll know what's poisonous, unless...
Render Poisonous- make the things flesh (or fiber, see below) carry an on-consumption poison. This gets into your cattle, hope you notice it.
Syndromes the Effect Plants- Never plant anything but Plump Helmets? Just wait for Plump Helmet Rot to destroy your fortress. Or to make them poisonous.
Plagues- if you have disease syndromes, let there be a toggleable feature that causes a special "Plague" event- a single dwarf gets hit with an infectious syndrome, and your fortress has to deal with the results. Could be tied to fortress cleanliness- drinking murky water ups the chances, or exposure to miasma. Plauges could be procedurally generated, or half a ready-made list included in the raws.
Plauge Pits- so, I'm being self-indulgent here, but I love this idea. Have a few sealed-off tombs underground, maybe with clear borders (constructed walls), maybe without, that include a small amount of treasure, a lot of corpses, and some infected blood with an extra-nasty disease. Imagine that with a Rage Virus- one that causes dwarves to go berserk and spreads through blood/bites; you break open a pit to find a pile of mauled, mummified corpses, and seconds later your miners start tearing eachother apart as you race to quarantine the rest of your fort. Too mean for vanilla? Probably. A modder's dream come true? Certainly.