Ok, this my first post here.
Dwarves are by far my favourite fantasy race, so naturally Dwarf Fortress is one of the best games I've ever played! How I found out about the game - There was a post about it at the Penny Arcade forums about 3 months ago.
Some bugs I've encountered:
#1 It takes ages for activated squad members to fill their water skins (not sure if only filling from wells is so time consuming). Squads can't quickly respond to threats if 'water is carried' is enabled. Another combat related issue, if a squad leader is sleeping, his/her squad can't fight. Since you can't forcibly wake up dwarves, you need to change the squad's leader to issue commands. There should be an alarm in the case of an emergency (which would naturally wake up squad commanders and un-injured squad members).
#2 Not sure if this is a bug, but it takes several minutes for a fresh siege operator to load a catapult.
#3 Troubles with bags. There's several bags with plump helmet spawns inside one barrel. Here's the troublesome part - Most of the bags only have 1 plump helmet spawn in them, and one bag has several pages worth of spawns. I rarely have bags free for for ex. flour or plant extracts. The dwarves should check if there's a bag with the type of seed they're carrying before starting filling a new bag.
#4 If you're placing a statue in a corner, the dwarf placing it often gets stuck under the statue and can't move from under it.
#5 Carpenters can't make animal traps if their trapping skills haven't been enabled.
#6 Migration and encountering new neighbours has stopped after the second year. I pray my current fort hasn't been ruined. As a side note, I've never seen any cave lobsters except imported ones, make them more common please? There's no huntable animals in my current zone either, which isn't a big deal.
#7 Dwarves that have cleaning skill enabled, and there's a lot of blood, ichor and puke in the fort, they rarely clean up anything. Do they need soap?
Hope these help, keep up the fantastic job, Toady!