Well, two ideas I had.
One, a fortress built into an isolated mesa. By that I mean, a hill with a flat top.
Specifically, I thought it would be cool to find or make such a large hill, with forest on top, and remove the upward slopes all around it. In other words, remove any way for people to get to all the nice woodland area on top... except via your fortress. The point would be to have a safe area for above ground farming/ tree chopping. Combine with an underground river source of such, and some good vantage points over surrounding flat ground for archers, and you have a pretty nice seige base for when seiges roll around.
Two.. hmm, this one might have been done, but... I was experimenting with this the other day, and didn't fully finish the job. My idea was that you make a fake lake next to a river, without filling it up yet. Then dig your base entrance down from the lake bed, with plenty of room for trade caravans to get in. Set up 1) some water tight gates at your base entrance/trading room, maybe a few more than one, 2) a v. large underground empty water holding tank of multiple z-levels, 3) shafts running from the base of the lake to the holding tanks, with water gates, 4) shafts connecting the lake with the adjacent river, with water gates, 5) a central control room with levers for all the gates.
OK. So, the idea here is that, for coolness factor more than anything, your only base entrance is completely hidden underneath what appears to be a normal sized lake/pond by a river. With a few switches, water sucks down suddenly, and your base entrance appears like the evil lair of a James Bond villan. Classy.
You could even use it to drown raiders if you times it right, combined it with some extra purpose built drowny rooms. Also, the holding tanks could then be used for farming/drinking/waterfalls/etc.