Tribble Cannon - Send tribbles to your enemy, they lose energy as their resources are devoted to fixing this problem.

I like the idea of the POW module, but also refugee. Able to scoop up crew that may not have otherwise survived the fight, could improve relations with other species if they're returned. Or, you know, ask the prisoners some difficult questions, with duct tape and jumper cables.

I'd like to see different designs for modules. Bio-mechanical versions, purely mechanical, crystalline, etc. Having different designs but similar capabilities. 

Boarding crew - similar to Orz, or instead of killing can convert members of the opposing crew to come join, reducing their and restoring yours.

Phasing - Can be used in map or in melee, lets you pass through other objects for a brief period of time (avoid attacks, or avoid encounters)

Kinetic Displacement - reduces a %% of damage recieved, and converts it into energy for your ship

Modules to enhance your fleet, shields, velocity, inertia, etc

Targeting System - Doesn't home in, but will show LOS for weapons that can't be homing

Bio "Recycling" plant - strangely looks like the druuge furnace, break down biological material for resources instead, such as fuel. Pairs well with prisoner jail

Turn signals - Comes in with 22 generalized directional pointers

^ This guy gets it.

Love it: "I'd like to see different designs for modules. Bio-mechanical versions, purely mechanical, crystalline, etc. Having different designs but similar capabilities."