I have a particular fondness of building hybrid forts with below-ground living and production and a huge above-ground defense. It may have to change in the new version since I've never had to deal with flying enemies before, besides wildlife, damn those giant cave swallows. Anything particularly interesting you can think to do without flooring over your fortress would be great knowledge. also excluding the following:
You could build your walls to the top of the map since fliers cant leave it to go over them, have your fort be like an open-topped citadel. More stone, but incredibly awesome, especially if the interior is entirely used up except for a courtyard/pit in the center. A very basic stone outer wall and underground caravan access w/ cave in for blockage would be prudent during construction. Bonus point if your finished entrance is guarded by a obsidian caster hallway
(hall with multiple obsidian caster pairs, water on one side magma on the other) all in glorious obsidian blocks (need to change melting point to above 12.5K to prevent horrible death)
If you set up your first obsidian farm extra early you'd never need to stick your pick in anything deeper than the first layer of soil. Hard to find a flat, volcano-blessed landscape though...
In my most recently genned world, there was a mountain peak adjacent to/as part of a non-mountain region inside a mountain range. If enemies EVER even show up from above ground, I'd have time to prepare in peace, as well as another interesting place to build my super-tree mega-project (requiring abandonment of the current one). Not to mention having tons of z-levels leading up to the peak. Put world tree INSIDE citadel. Elves must be washed (with soap, just to make them angry) before entering past depot.
Excuse me, I seem to be rambling incoherently.