Generally, command modules contain no special features, but occasionally, pilots install lasers which can fire when exposed. The Nemesis (Captain Forever), Eris (Captain Successor), and Charon (Captain Jameson) are examples of this. In the case of the Nemesis and Eris, the base laser fires at 2 Hz (making it equivalent to a Bravo laser). The Charon has a custom laser which fires at 500 mHz, four times as slow. The Dawn Star (The Dawn Star), unlike the Charon, has a laser that fires at 4 Hz, eight times as fast and twice as fast as the other ships.
Other command modules are equipped with special mechanics. The Narcissus (Captain Impostor), has a special machine which allows cloning of other ships. More importantly, the Nemesis, Eris, and Narcissus all have a special device which uses "self-correcting harmonics" to institute immediate repair of the command module when it is destroyed; the resulting explosion wipes out all life in the sector, but means the pilot can resume flying immediately.
The primary way to obtain parts for a ship is to destroy an enemy ship's command module. Any modules that survive the battle can then be picked up and attached as desired before moving out. There are some ships that do not drop any modules; aside from the Nemesis and Eris, station guardians in Jameson disintegrate upon command module destruction, unless the player finds them as "derelict", meaning the ship is inactive and can be destroyed at will.
Especially in higher tiers, it is very wise to have all four sides of the command module protected; that way, no errant shot can hit from behind or the sides.