Goner Truelight Seeker: This ship can be obtained during
Goner plot. If you follow the questline you have to cap it (or claim it); as soon as you do so, the Goners regain its control. At this point you can either finish the whole plot to get it as a reward, or go hostile and board it again (this time stealing it from goners instead of pirates) - In recent patches the result is the same (You won't have a second
Truelight Seeker as a reward if you already stole it), however if you double-captured it in early patches the
Truelight Seeker remained invincible, even when upgraded to 3.1. Invincible ships can't be Reverse Engineered so if you are starting in early patch to get all ships and want to get all blueprints also, don't double-board it.
Invincible
Pirate Blastclaw: It could be claimed in early patches during the same
Goner plot, in very last stages of the plot you have to follow a
Blastclaw, which reveals a pirate base in
Gaian Star, which you have to blow up later on.
If you manage to finish the plot (blowing the station up) before the
Blastclaw docks, it remains ownerless and thus can be claimed. Here's how it's done:
You need a fast ship for this part of mission, if your relations with pirates aren't too good, it has to be a strong one too. 250m/s overtuned
Hyperion Vanguard did the trick for me. Also you need to get the 35 Space Weed and 60 SQUASH mines in your cargo bay beforehand. Jani Hall escapes from the Pirate Station once the
Blastclaw is within 5km from it. At this point what you have to do is speed up and engage the
Blastclaw. After few shots he will turn red, effectively forgetting about his docking orders, and start chasing you instead. As soon as it happens, go pick Jani up, and start flying away. The
Blastclaw will follow you; keep fleeing until you've dragged him far enough, so you have time to complete all the remaining steps of the plot before he manages to return to the base (60 km was enough for me). Just jump to
Elysium of Light, get close to the
Ozias and, after the plot advances, return to
Gaian Star and keep following the steps in the plot. After Pirate Base was blown, the option to claim the
Blastclaw appears. It was still red in my game and kept shooting my
Hyperion Vanguard but I managed to sneak from behind and claim it (at which point it stopped shooting).
The "claim" option won't appear in patch 3.1 EDIT: not true, it's still claimable, just need to wait couple of seconds after destroying the base. It won't be invincible anymore, though.
Argon Griffon: You will still get rewarded one of these even if you complete the Operation: Final Fury in early game version and then patch your game to 3.0 or 3.1. Tested this behavior for games started in 1.3 and 2.5. For a walkthrough on the Operation: Final Fury look
here