Goldfish: Bulletpoint - Fast, pointy, painful. Therefore the name was put together from "arrow point" and "bullet." Also, it's fun because of the actually rather peaceful original meaning of "bulletpoint".
Pyramidion: Ever Onward - Because of the charging nature of the ship. Also, this name has a rather heroic ring to it which I also find very nice.
Squid: Jolly Dodger - as reference to the Jolly Roger and the maneuvrability of the little guy. She used to be called "Why not Zoidberg" though. Because Zoidberg is somewhat of a squid, I guess?
Junker: Belly of the Beast - A great name, I find! She might not be very beautiful but damn, she can pack a punch! Also, I like greeting my crew with "Welcome to the Belly of the Beast!", whenever I start a game.
Galleon: Salacious Maiden - She has some really nice big guns. And she really enjoys you playing with them - if you know what you're doing.
Spire: Double Helix - Thanks to the spiral staircase and the long and narrow shape. A reference to the Form of a DNA strand.
Mobula: Steamroll - due to its general shape. I am not really satisfied with the name. Doesn't matter though, as I am not flying it anyway at the moment.