I started naming my ships after ship names from Iain M. Banks' novels and also started making up new names that fit the theme.
Junker - Clear Air Turbulence
Even when the skies are clear you might encounter some
Squid - Levity and Mirth
Happy ship, happy name
Mobula - Congenital Optimist
"Hydrogen will save us, right?"
Pyra - Demiurge Engine
The creator of all things evil, and the burner of engines.
Gal - Gunboat Diplomat
"You see that ship right there?"
Spire - Irregular Apocalyplse or Dorsal Tesseract
Sometimes your gunners hit things, sometimes they don't
Goldie - Vivacious Inquisitor
It's small, it's red and it's angry
EDIT: explanations