I've run into this problem. See, while the Goblins haven't come for my delicious cheese in mass, they've grown bolder. Mind you, this fortress is 5 years old, so that alone is a surprise. I have my defenses set up so that the only three ways into the fortress would be:
1. Main gate. Which is on a cliff with ballista battery, cage traps, and a retractable bridge. The entrance is elevated so the only way to the gate involves going up a ramp and crossing the bridge.
2. Aqueduct. Waiting for the river to freeze, tunneling up into the aqueduct and destroying the pumps, then climbing through and destroying the grates. Impossible for sieges. (I know, I built an aqueduct on river that freezes over yearly.)
3. The back door. The aqueduct runs through 3 levels of my fortress, fills my water reservoir through a controllable floodgate, and then drains off the map. The back door uses floodgates to isolate a portion of this drain, stopping the water drainage and opening a 1-wide passage. Flooding of this can be resumed at any moment. The passage itself is loaded with cages.
Now, I have a few prisoners from "incursions." Should I build a more elaborate drowning chamber to deal with them, or work on a "better" defense system to kill future prisoners, and leave the mutilated bodies for all to see? I was thinking build a designated water storage for the chamber, with a way to pump water into/out of at will?