This is where you'll spend all the mirian you've been hording. Siege Defenses are costly affairs, but the good news is that they're permanent- even if you lose and retake the fortress, these babies will be waiting for your return. Note that, like skill upgrades, you can only have one of these special defenses active per captain (eg you can have poison nozzles or flame nozzles, but not both at the same time).
While various defenses can be matched against the weaknesses of various attacking forces, an overall winning combo for any fortress is Spiked Walls + Metal Walls + Poison Spouts. This trifecta will keep enemies outside your fortress for as long as possible, taking damage and reeling in agony all the while. Use this gift of time to convert or kill enemy beasts, then convert or kill enemy captains while they're still conveniently placed outside. Even if you don't manage to take care of each one singlehandedly, they'll be in pretty poor shape by the time they breach the perimeter- easy pickings for your own captains.
(Note that spiked walls prevent you from leaping up the walls as well, but you can bypass this by leaping up tower corners, or Shadow Striking an orc on top of the wall)
Other generally good defenses are the Cursed Siege Beasts and the Hunter Host. Curse is one of the rarer status effects- very few captains are immune to it or enraged by it, and while the hunters aren't that damaging, their spears are ideal for interrupting the actions of enemy captains, leaving them vulnerable to your own defenders.