I think it would be cool if you could self-destruct Hostile Ships when your done killing all the enemies. Set up a computer to rig the hostile ship to blow up and give you enough time to escape the explosion.
Nice idea! I blew up the Avian's ships with bombs on beta version. (unfortunatelly i can't play Starbound on my computer since it's using OpenGL, I don't ever have much knowing what is avaible in game already )
Or have a weapons panel on your ship like the one for mechs that allow you to engage in a "space battle" minigame. If you win, the enemy ship is destroyed you get a crapload of salvaged parts. If you lose... Your ship takes on a new damaged appearance and you have to spend loads of money or parts to repair it.
I did think it was a shame that you couldn't dismantle the things, sorta expected there to be a shield generator on board providing block protection. To build off the above suggestion, ship battle mini-games. The old X-com games had a decently simple mini-game for shooting down ships that could work. Rather than receiving a loot bag for winning, what if those ships spawned a "dungeon" so to speak? Shoot em down in space, they make an Anomaly type zone, shoot em while orbiting a planet, and you beam down to find the wreck somewhere on the surface as a new dungeon. As for the losing scenario, all that loot we get from mech anomalies now could have another use. All those hull plates, copper wires, silicon boards, ram chips, etc could be used for the repairs. Edit: This could have the side effect of fleshing out and tying together some of the "secluded minigame" issues people have brought up, such as mechs only being used to explore maps for mech parts to survive in better mech maps for better parts etc. Now parts farmed commonly from mech maps can be used to repair ships, the anomalies can be tied in to ships shot down with the ship battle minigame, the "peacebringer" upcoming feature could request you to shoot down ships.
Or capturing the ship for colonist trying to peacefully resettle. You could get a bunch of pixels as a reward and a gift basket or something. Or choose to salvage it and get a bunch of scrap.
A ship battle minigame would be more interesting, specially if the Player could also collect parts from destroyed ships in order to enhace their own, could build more ships from either salvaged or newly-made parts (The latter would be very expensive, of course), and could switch between each other or have them manned by recruits so they are also controled in ship battles.