Were-creatures, evil biomes are awesome, necrospammers, clean rivers, mining changes, smelting/masonry rewrites, clothing and er... Probably some other stuff I'm missing. What'd you want to know about first?
Were-creatures are poor fellows who have been cursed by the gods or some such to assume the form of a randomly selected animal every full moon. In Fortress mode they're relatively harmless, since they arrive ambushing it's possible to miss them entirely until the full moon ends and you discover a very scared naked person. If on the off chance it bites a Dwarf or you capture one, they can be invaluable in making a special were-creature squad which is only vulnerable to one metal (I've seen were-creatures take steel bolts to the head and shrug them off because "other arms may not cut so deep"), which heal every full moon (even lost limbs!).
If they happen to bite a Dwarf and you not notice this, you may be in for some fun.
Evil biomes can resemble what they did in .31 with purple fauna and corpses wandering on to your map, but now there's an addition of weird tentacle grass (it moves! - serves no purpose than to look putrid though), possible evil interactions (which cause dead bodies/body parts with an eligible [GRASP] tag to come back to life), deadly/harmless rains that could consist of RNG liquids, creature blood and may have a nasty syndrome attached (which can cause anything from necrosis to unconsciousness) and finally the eerie glowing mists.
These can have the same effects of evil rain, but come in rolling clouds (much like miasma - but more mobile) and can also cause things to transform into husks of their former selves... Needless to say, they are terrifying to deal with by that point.
Necromancers have also been introduced, with towers occasionally popping up in world gen (or they take over a neighboring town). These can be visited in adventure mode, or if embarked close to, they will siege you with zombies/sometimes necromancers and may send stealthed necromancers. Needless to say, they are dangerous if left unpunished. Guard your refuse stockpiles.
Rivers used to stagnate (in the update) due to a bug, and now clean water destroys stagnant water.
Mining no longer drops stone/ore based on the miner's skill, but now carries a 25% luck chance of dropping stuff. More often than not you will not dig as much stone/metals than you could've in .31, but smelting now gives more (400%) bars and making rock blocks has the same bonus to production. Adamantine is unaffected (not using the mining skill at all), whilst gems have a 100% drop rate now.
Dwarves also wear clothes now, and will most likely go insane if left naked for too long.
You'll probably want to look up Kivish and his mother (Asmel?) for some info on were-creature syndromes and how they are spread. LoudWhisper, have you determined if Kivish is a were-civit yet?
Kivish is 100% Dwarf, the possibilities...