I'm pretty sure this wouldn't be too hard to implement: a way to take notes for yourself. It would be nice for keeping track of plans for expansion, or problems you want to come back to, or even what lever does what. And it would be especially useful for coming back to a long-neglected fort; I know it takes me awhile to figure out what's what when I haven't played a fort for a week. This would also be great for succesion games, since you could leave notes for the next ruler; likewise for adventure mode. I know I can use a paper and pencil, and I have, on occasion, but it would be ideal to have it in-game.
The way I imagine it in simplist form, is just a screen with a text box. The text would get saved along with the fort. It might be a little tricky to make it so you can move your cursor around the text (to edit and delete), but well worth it I would think.
For bonus points, or further down the line, make notes attached to any building/item/dwarf/whatever. Basically from anything you can look at, you could also access a note screen for that thing (sort of like the [y]customize screen for dwarves). All your notes would be visible from the main note screen, too. You could also leave notes not attached to any item, but just with the camera on a certain spot, like the map archive's Points of Interest. From the main note screen you would have a '[z]oom to object/location' command, which would work just like the 'zoom to creature' command on the units screen.
I'd be happy with just a text box screen, though. Then I could write down how many bedrooms I have ('til a bed-counter goes in).