I don't think I will ever tire of seeing more games that let you build your own spaceship, BlockShip Wars: Roguelike added Linux support recently.
It has two game modes available, the first is what they're calling "Roguelike mode" featuring permanent death, no levelling or experience points and the other is the "RPG mode" which has experience, levelling and so on.
Have a look at the trailer:
I'm not a big fan of the graphical style, personally I think it looks really bland, but if it makes up for it with the combat and ship contruction I could look past it. I mean, I've seen a lot worse.
It currently features over 50 AI enemies, each one made out of blocks just like your own ship. There's more powerful boss ships, 18 special abilities to give you an edge in combat, massive randomly generated maps to explore and so on.
Find it on Steam.