This will probably sound lame, and something that also makes me unoriginal, but I happen to be a very big fan of Admiral Kathryn Janeway. With Voyager as my favorite series, and the series which cemented me into Trekdom as a whole, I have always admired her as a character and female role model. I named my ship the U.S.S. Janeway in honor of her service in Starfleet. I even have the Intrepid class so I feel like a real Voyager geek.
USS Revenge (Assault Cruiser)
Actually, I got the idea from Edward Teach's ship, Queen Anne's Revenge, But...
In my Eng's story, his Grand-father (also a Starfleet Eng) died fighting the Borg at Wolf 359.
USS Miss Catalina IX (Captain's Yacht)
and USS Catalina (Exploration Cruiser Retrofit)
It's where I come from. The SS Catalina is a big part of our history and the Miss Catalina boats were a series of wooden speedboats who also have their history in my hometown. There's only been VI as far as I know, but I could only use 2 characters for numbers, so I said, "hey... it's the future..."
Hence the 9 ;-)
USS Pisces (Starter Cruiser) - From created Zodiac Class Cruiser created with Traveller High Guard rules.
USS Detroit (Cruiser) - Where I am from.
USS Nikki Indigo (Heavy Escort) - Because I miss her.
USS Nikola Ross (Exploration Cruiser) - Because she is in my prayers.
USS Starhawk (Advanced Escort) - Favorite line ship created with Traveller High Guard rules.
USS Decrepit Coot - Retro fit defiant class. She's my baby.
I picked this name because I found it funny to have an escort with immense destructive abilites with a name describing a broken down old bag 'o' bones. Just don't tease her to much or she will force herself on you. AND YOU DON'T WANT some very old woman forcing herself on you. Unless thats your thing.
No offense to women young or old. For the sake of argument though, ships are generally gender specific to females. Ships tend to have awesome curves, very much like women.