Apocalypse How: Sol suffered Stellar/Physical Annihilation in the backstory, with Planetary/Total Extinctions and Partial Extinctions to most other planets in systems within the blast radius. Ouch. Plus the plagues on Sorom.
Arbitrary Maximum Range: Projectile/energy weapons fade out, missiles presumably run out of fuel... yep, limited ranges all around. Justifiable with everything except kinetic energy weapons like gauss guns.
Attack Drone: House Za'lek doesn't have the manpower to waste on the classic Space Fighter, or otherwise find them wasteful. Or something. So instead, they use squads of small attack drones. Also, the Collective.
The Battlestar: Since, similarly to Escape Velocity, you can mount a fighter bay to any ship provided it has enough computer capacity and an empty equipment slot of sufficient size, the biggest, most dangerous ship of every faction tends to be this.
"Sorom was caught in the blast and was rendered sterile. But elsewhere in the galaxy, the Soromid persisted. All Soromid knew the history of Sorom, and they would not suffer to be destroyed, no matter what the universe threw at them."
Future Imperfect: An archaeologist in one sidequest theorizes that a skateboard might be a religious artifact.
Gatling Good: Several types of Gatling weapons, most of which are quite useful in combat. A decent build for the Pacifier destroyer is two Mk3 Laser Turrets and a Turreted Vulcan Gun.
Hyperspace Lanes: As in Escape Velocity, hyperspace travel is restricted to explored links between nearby systems. Naev further restricts travel to jump points, whereas in EV you could jump anywhere in a system as long as you were far enough from the center.
Klingon Promotion: Combined with retirement. Dvaered Generals take a small contingent with them when they retire and become a Warlord governing one or more planets that they 'acquire' themselves, usually by knocking off an existing Warlord.
Legacy Character: The Kestrel appeared in Escape Velocity and EV Nova, and now in Naev.
Space Is Cold: Averted. Management of weapons heat is part of combat. As your weapons heat up, they lose accuracy, and when an outfit or weapon maxes out in heat, it fails and has to cool off. Weapons and outfits transfer heat to your ship, which radiates it into space. The hotter your hull gets, the more visible you are (which plays out as enemies shooting at you more). You can enter a rapid cooldown mode if need be, which radiates all your heat at the cost of you being immobilized for the duration.
Space Is Noisy: Very noisy. If you can't hear gunfire at any given moment, then you're either in the starting systems or the Nebula.
Played with. You can drift in one direction with thrusters off, but to maintain full speed you need to maintain thrust. (Let go of the accelerate button, and you'll slow down a little and then stay at that speed.)
In the pirates defense: Yes, they attack everything in range, even if it a huge cruiser. But they do break from combat if they get down to around 30% hull. They then fly to the nearest jump point to escape.
Super Soldier / ‹bermensch: Soromid don't exactly get along too well with the rest of humanity due to their enhanced capabilities and appearance. Or more accurately, the rest of the galaxy doesn't get on too well with the Soromid. The Soromid could care less.