Superweapons are weapons not fired by units, but from buildings or even from the sky. Superweapons usually have a controlling building you have to build, which then enables an icon on the sidebar that counts down. When it's finished, you can click the icon and target the weapon. The weapons tend to do a lot of damage with no risk to the player who fires them, often making the difference between victory and defeat.
Superweapon behaviour is hardcoded, only the art assets and warheads can be modified.