I don't honestly think either of these are particularly good ideas for DF, but they could be in some form.
Reverse Breadcrumb Pathing : When a dwarf decides to go someplace, he places a breadcrumb, or in this case, a +1 pt cost field, on the squares of his path. Other dwarves will try not to path along his path (unless they are following him to a destination, which I assume is a pathing shortcut in the system). This means less traffic jams as dwarves naturally path around each other. (This is most useful for dwarves running down those one wide exploratory tunnels to pick up stuff.) This could be combined with a flow indicator to create a tendancy for one way traffic down a hall (Or right/left lanes in two wide hallways).
Waypoints : Allow (Players to request) dwarves to build signs. Whenever a dwarf at a defined location (I'm thinking piles or rooms here) is engaged in pathfinding and it finds a waypoint, it records that distance (but maybe not the actual path). Each waypoint retains a path cost (and maybe path definition) to each other waypoint. (I'm thinking 5-6 would be ideal, your front gate/trade depot, the stairs from the 'depths', the well, the apartment complex, and maybe the workshop area). This information is maintained at the same time the dwarves re-path. (Basically pathing signs(signs-1)/2 extra paths, which is 15 for 6 signs)
OK, so when the dwarf finds the path to a waypoint, it then knows how far all the other waypoints are from it, and, if another unit has pathed to the waypoint from the spot the dwarf is going, it also puts an upper bound on the length of the path between the points. This isn't particularly useful if your waypoints are bad/close together, but if you've got your zones widely spaced, it could be a big help.
Some code possibilities:
Compare the path known to the as the crow flies distance. If it's reasonably efficient, just use it. (I.E. if the linear distance is only 80% of the pathed distance, just use it. Since the path between disparate waypoints is going to be calculated once, you are saving that cost each turn by the number of units that actually take that path-1. Minor deviations to get out of the way could be supported.
I'm not sure how the pathing works. The simple solution would be breadth first of all the available points with a bias for moving towards the finish line. (or a depth first with a bias towards the finish line) However, having a guaranteed max distance based on the waypoints could give you some optimization here. (If you want all mathy, it would be an ellipse looking thing saying how far you could path from the straight and narrow and still hit your target). This would allow some more 'risky' pathing solutions to be tried, because you'd have a guaranteed cutoff point.
All of that is based on my experience of having a few areas of dwarf concentration seperated by big distances. (Crafts and Trade upstairs, apartments to the right, farming to the left and the Smithies downstairs, with the mining down in the underdark)
Again, don't know if they'd work for DF, but it's the fruits of my thinking about optimization and it interests me