Miranda refit: All come equipped with a Genesis device, allowing them to destroy every ship that does not have a Vulcan Bridge Officer.
Constitution-refit-refit: Has been refit so many times that there are systems buried in this vessel that nobody even remembers were installed in the first place. Has a special button you can push will cause any number of helpful or harmful effects. Sometimes your ship explodes. Sometimes you fire an insta-kill phaser beam.
Sovereign-refit: can fire a volley of quantum torpedoes. Ship however can never finish a battle above 50% hull.
Star Cruiser-refit:A swarm of R2 units can repair the ship mid-fight
Dervish-refit: Can cause flame wars on contact
Prometheus-refit: Can be piloted by an EMH and will perform better then possible while under the control of a player.
Luna-refit: Has a Horta engineer like in the Titan books. He doesn't do anything, but he is there.