Well I had the Trantor named after the capital of the Galactic Empire in the Foundation Series.
Then I had the Majestic which was a name generator ship, just happened to like the name.
I had the Merrimack because I live in New Hampshire and that is the river that flows through Manchester.
Then, I ended up with the USS Walter C Wann because it was the ship my grandfather served on in WW2.
I gave up trying to think of name for my ships, I just use the default one.
The only problem with that is that I it takes a while for me to remember that name. So in one mission I was told to return to the Taxolan and I spent a good five minutes looking on the map for a place called Taxolan. Only to get red faced when I realised it was my ship.
I named one of mine the Sanctuary, and did the same thing the first time I was told to return to the Sanctuary.
I wanted to name my first two Merrimac and Monitor (the Civil War ironclads), but it wouldn't allow "Monitor". So I have the Merrimac and Mentor. And I'm mildly disappointed.
In order of which I obtained and named my ships: Scotland, Edinburgh, Glasgow, Dundee and finally Aberdeen. All my ships where named of course after Scotland itself and its 4 major cities. I'm not a scotsman but I am of scottish descent and I identify more so with the small amount of scottish blood that flows through my veins than anything else.