I've been looking at ship designs, and there seems to be 6 modules that you can't mount on your ships in the ship designer, but they may be found on some of your default ship designs. I'm using the Terran Alliance names for the ship names:
-Militia Barracks: +50% hit point while in your territory (Defender)
-Antimatter Bomb: Damages fleets within explosion radius (Fortress)
-Repair Drone Bay: Unknown effect (Battle Hammer)
-Integrity Field: +20% fleet armor (Battleship)
-Missile Disrupter: +20% fleet point defense (Destroyer)
-Field Generator: +20% fleet shields (Cruiser)
I also want to point out that the Fortress has a design flaw. Because it requires an antimatter bomb, you can't build one until you research your way far down the missile weapon techs. Normally, for other ships, they show up once you have both the techs for the hull size and basic weapons for the weapon type they use.