I unlocked the second engi layout in the process of that last run I just did. It's interesting - you only start with a single crewmember and you don't have a sensor, so your own ship is invisible to you. But you get better guns, and some internal drones.
Also unlocked: federation cruiser (you get 4 crew members at the start) and the rock cruiser which has some special armour that gives a 15% chance to avoid hull damage. I unlocked the stealth cruiser yesterday. That has a cloaking device, but no shields. I think I'd rather have a shield to be honest, because that cloak only lasts 5 seconds.