Well, my Krait-II is Xeno's Paradox, which I thought was quite clever. However - some of my other ships:
My I-Cutter has the Azure paint job and I named her Ice Queen, but after ONE pax mission with it I renamed her Dammit Turn Already.
My Beluga was originally named Emerald Windancer but after discovering how well it enters Stations, it was quickly renamed 1-ship Mailslot Block.
My Corvette, which is actually named HMCS Algonquin has recently - after loading a ton of G5 frags onto her - been re-named Male Overcompensation.
My T-9 was Continental Drift and was recently renamed Hippoposthumous.