O know that is a general title, but I have a few ideas.
Automatic Track/Mine cart use:
To be honest have played with, and failed, to program my tracks and mine carts. Also, I realized, that even if I had gotten it to work it was not really very useful. A track has to be used for one material (to my understanding) - for example shipping stone from a stone stockpile to a workshop. Why not just build a few wheelbarrows?
It would be easier if I just put down the track, or two side by side, and assigned a mine cart to each track and let the Dwarfs use them anyway they wanted. Of course, being Dwarfs there is a chance they may drink and ride. And there may be a slight chance for a accident but to be honest I think it would add a little to the overall enjoyment of watching the Dwarfs do their own thing. And one less thing for people new to the game to figure out (creating, training, and dealing with the military is, in some ways, bad enough. Oh, I figured out how to - but barely). A complex game can be fun - till it becomes too complex and no longer fun. When a Dwarf Fortress becomes huge you want to use the time and vast resources for major engineering projects - not micro-mange everything the Dwarfs do.
Canals:
I noticed somebody posted about boats. And there was a debate about sea traveling Dwarfs and such. I was thinking something smaller. Like canals that can have horse or animal pulled barges. Like those used in Europe and America before the railroad took over. It would have to be a special command, not just digging a 'channel' with h, require stone (to keep the banks from falling apart), and a Animal Tender. There would need to be enough room on the side of the canal to allow for a side-track for the animal pulling the barge.
Of course, the barge would have to carry enough to make it worth thinking about making. And it brings in the idea of locks - and Locktenders - allowing for barges to be moved up or down hills without being damaged. I guess you could make a gravity powered canal but there are dangers to such things. I can see a lot of players having a LOT of fun with this idea. This would also give players a reason to keep and tame/train animals that they may otherwise just butcher for meat. Like horses. They canal workers, whatever name is used, would have to care for the animals, and lead them down the side track.
This does bring up the idea of using large animals, properly tamed, for pulling carts in the mine or maybe helping drag back fallen timber. But I think I will stop with these two ideas.