Here's a list of most of the ones I can think of off the top of my head. Health-related stuff is
bolded.
Fortress Mode*Every map has magma now
*Titans and some other megabeasts and so forth are procedurally generated now so that each one is different (Although many of the standardized megabeasts such as Dragons and Bronze Colossi still occur as well)
*
There are some new nobles, such as the Chief Medical Dwarf.*Some old nobles, such as the philosopher, no longer occur, and several others, especially the Dungeon Master, which are supposed to occur will often fail to show up
*The military interface has changed significantly. See
Military,
Scheduling,
Squads,
Military FAQ Supplemental Equipment Information and
Attacking on
Magmawiki*
Care for wounded dwarves has been greatly expanded.*
There are several new healthcare related skills/labors *
Hospital zones can be set up now, and stocked with beds and traction benches to rest injured dwarves, as well as chests and bags to hold thread, cloth, gypsum plaster, and soap for suturing, wound dressing, bone setting, and wound cleaning respectively (although the actual stocking of these items is still a bit buggy). I think you can also reserve water buckets for hospitals too, IIRC*
Hospital settings are set/changed by going into the zone ('i') menu, moving the cursor to the hospital zone and pressing 'H' *
Traction benches for wounded dwarves may now be constructed at a mechanic's workshop.*
There is also now an advanced HEALTH summary screen accessable from the fortress overview menu*You can now make rock, clay and/or wood pots which can fulfill most (but not absolutely all) of the roles of barrels. (Clay pots must be glazed using ash or cassiterite, however, before they can be used)
Adventure Mode*Also, adventure mode combat works differently. You can now select which of the enemy's body parts you want to attack.
*towns are laid out much differently
*Sleeping outside of a city may result in being attacked by the bogeyman (or bogey
men)
*As mentioned previously Titans and some other megabeasts and so forth are procedurally generated now so that each one is different (Although many of the standardized megabeasts such as Dragons and Bronze Colossi still occur as well)
*The map key has been significantly changed, (to the point where I, personally, find it just as unreadable as I did when I first started playing.)
Legends Mode*I think that a wider range of information can be exported from legends mode now