Well, as for ship names, try to think of what you want people to think of when you tell them its name. The 'Millenium Falcon' sounds like a fast ship. It can take your cargo from here to there faster than the other ships.
'Serenity' was named after the Battle of Serenity Valley, a place where Mal (the main protagonist and Captain in the show 'Firefly') holds a lot of value and memory, a reminder of what he's lost.
'Bebop' doesn't really mean anything, overall. It evokes a style of music and a lifestyle of a time gone by, but also elicits a kind of frenetic energy, I suppose, as well.