So far, here's what's come up:
The major 'problem' is that dwarves don't always do things in the order we want them to. While this is usually possible to micromanage, it takes away some of the fun of playing large fortresses. These fall into two catagories. Dwarf priorities and Task priorities.
Skilled Dwarves will perform low skill tasks(hauling) rather than their assigned tasks. When these tasks are removed, they grow bored or are idle. (As there aren't enough skilled tasks to keep them occupied)
Fish, meat, skins, fat all spoil. There is no way to make sure that these jobs get accomplished in a timely manner if the dwarf(s) with these jobs are also performing other labours.
Rare and unusual jobs (like architecture) don't get enough use to keep them busy. It's usually going to be a side job. There's no way to keep these dwarfs occupied without massive micromanagement.
Eating. Military dwarves will decide if they are hungry or not when put on duty. If they are, they'll eat before heading out. That's backwards. On-Call dwarves should eat when nothing else is up, but be willing to go hungry when the emergency fires are lit.
Certain order important tasks are done in the wrong order (usually mechanics). Sometimes you want to build the windmills and mechanisms before you build the axels. Also useful for build from the inside out type tasks. (No walling yourself in)
No way to specify 'deep' exploratory mining versus the rooms you need now.
Pull that lever NOW. Sometimes there are fort emergencies. At the extreme level, this includes the desire to have a civilian run across 1/7 magma while be chased by a werewolf in order to pull the fortress lockdown before he's gibbed. At a more sane level, just being able to say 'grab the closest dwarf and assign them this job' would solve a lot of heartache.
Naturally low priority tasks may stagnate
Cooking. There's food ready to be cooked, but the cook is resting, partying, hauling rocks, or hunting for vermin.
Miners will occationally grab jobs across the map from them rather than two squares from them. Conversly, a miner will decide to work right next to the other miners, claiming an important square for the duration of his trip across the map.
There are a number of suggested fixes discussed below.
List all open jobs in the jobs screen in order of priority, and allow users to find and change individual jobs
Skilled versus unskilled. Dwarves do skilled tasks first, then unskilled.
Allow user to set priorities, either by number, or high/mid/low for a dwarf
Allow user to set priorities, either by number, or high/mid/low for a specific job
Allow user to set priorities, either by number, or high/mid/low for a job types.
Profiles could be saved by Dwarf Job Profile
'Do Now' Toggle (on job screen) that grabs the nearest available (reassignable) dwarf and makes them do it.
Refactor code to make the behaviors 'correct' without giving player controls (I.E. hardcode solutions to the big problems)
Allow dwarves to 'steal' jobs from others when they are literally right there. (Mining right next to it). This is especially useful if one is traveling, and the other is using the high priority 'grab contiguous square' command.
Economic Simulation: Dwarves are already encouraged to do some jobs over others by the differing pay rates. Allow dwarves to be responsive to this
This has been discussed as far back as 2006, but seems to require a major rewrite for the way tasks are assigned to dwarves. That means a lot of work with 'only' the benefits listed above.
At least partially justified by: New Round of Top Suggestions Polls