This is going to make a lot of people roll their eyes so hard their corneas fall off but I usually name my flag-ship after my wife.
After that I will name my other ships depending on their role. My fast-attack frigates get names like Drake, Dragonfly and Firefly. My freighters will get called something like Bounty or Cornucopia.
For my cruisers and capital ships I have a specific naming scheme. The largest fleet I ever assembled had seven such ships named: Victory, Amazon, Medusa, Agamemnon, Alexander, Diadem and Bellerophon. I'll be very impressed if anyone gets the reference.