I know you probably know most of these already, but...
Listed twice:
bug #1376 - Presence of saltwater marsh causes mountain brooks/pools to become salty
Fixed:
bug #4025 - Every kobold starves to death at exactly year 4 in world gen
bug #1498 - Crystal glass items can't be made, CRYSTAL_GLASSABLE appears broken
bug #197 - No wagons in trader/merchant caravans
bug #1324 - buckets full of water were used to produce lye
Fixed in next release and marked as fixed:
bug #3453 - Baron/etc. cannot appoint baron-appointed nobles, such as the Dungeon Master
bug #231 - Body parts from large creatures (bones, meat, leather, tusks, etc) slow workshops down due to clutter
bug #4133 - Good/evil plants/trees don't appear (feather trees, glumprongs, sliver barbs, and sun berries)
Supposedly fixed in next release, but currently still marked as open:
bug #2481 - Dwarves will claim new clothes when theirs is worn (xClothesx) but not wear it
bug #3942 - Dwarves owning broken clothing. Clothes don't rot, ANNIHILATES FPS.
bug #535 - Equipping weapons/armor on military is erratic
bug #1451 - Military equipment interferes with civilian equipment (picks/axes/crossbows/quivers)
Supposedly/probably fixed in current/previous releases, but still marked as open:
bug #3708 - Ghost names that can't be engraved on a slab and nameless slab engravings
bug #3685 - Goblin squads invading a fortress will kill their non-goblin squadmates, sparking loyalty cascade
Probably
not fixed:
impossible mandates (slade - bug #782, blue jay tooth etc - bug #1623) due to strange preferences (wagon wood - bug #3676 etc)
While #782 is listed as "fixed", some people are still seeing impossible mandates (see
here), and #1623 and #3676 are still listed as "open". See also open bug #944 - Baron demands turtle shell door in dining room, and other demands of unattainable item/material combinations.