Something that occurred to me the other day, while driving in stop-and-go traffic during a snow storm; was that there seems to be a dramatic scarcity of water-usage for transportation. I know that dwarves probably aren't terribly sea-worthy, but I'm sure that the same species capable of incredible-machine-type goblin traps could manage at least a simple boat; (not to mention that there are other species, like eleves and humans which I'd assume would be more boat-proficient) Anyway, currently we are using rivers and such as water sources and/or for fishing; but we're ignoring another HUGELY important importance, and that would be their use for transportation. It's much easier to transport many goods via boat, than pulling them with livestock. I know that some of the various arcs talk about using rivers, etc, but think about this.
*shipyards
*hand-digging channels all over the map to transport large amounts of whatever on barges, setting up major ports and forging breathtaking trade agreements with neighbooring towns (which would be a bit abstracted, as you might not be able to "follow" around your clipper ship you've loaded up with tons of goods
*dealing with pirates
*having some species send boats to your town each year for trading.
*tossing chopped wood into the river and picking it up, downstream at a lumber mill.
*having people stop by in town on a river-ferry, just to visit (and stay overnight at an inn?)
I'm aware that most of these things are larger scale than "Hey guys, I've got 7 dwarves!" But I'm also aware of the draw of a large-scale project seems to bring around this place. Perhaps there could be preset shapes/sizes of boats (ranging from a small rowboat, to various sizes of flat-bottomed barges, to larger clipper ships... they could all just offer a 'platform' which you could then add things to, just as in your fortress... traps, ballistas, stockpiles, kitchens, fortifications, etc. (perhaps even the hold would default to a solid block, or a few different presents, and you'd carve it out... different sizes of boats would have varying #s of Z levels, which could be carved out. Also, these would use shit-tons of wood, so perhaps elves wouldn't build boats, unless they could make smaller boats out of metal, or pumice?
A lot of these things would require more of the economic arc additions, as well as regions and such; (what does having a large clipper-ship matter if you've got no where to send it?)
Also, people talk about building above-ground fortresses, but what about a large house-boat?
Sorry for the rambling, and hopefully I'm not repeating something that's been posted elsewhere... these are just a few ideas.
In one of my geology classes, we were talking about how at one time, Europe was this massive crisscrossing of man-made channels that were used to transport goods from one place to another.