My current main vessel is the USS Elysian, a Deep Space Science Vessel. It comes from the term "Elysian Fields" which has a relation to the heavens and what-not; perfect for space, especially uncharted and untouched space, which is basically a DSSV's specialty.
Other ship names I have had are the USS Murakami, named after a favorite author of mine. The USS Wayfarer, a pretty self-explanatory name. The USS Resolute and USS Emissary, both escorts and both with names that play off the Defiant name and DS9 in general. Then two early science vessels; a Nova-class named the USS Aurora and an Olympic-class named the USS Borealis.
I prefer to give my science vessels "ethereal" quality names, they seem to fit the purpose.
U.S.S. Cherokee -because I have Cherokee blood.
U.S.S. Cutlass -because it's a type of sword. (reassigned to the S.C.E.)
U.S.S. Endeavour -because it was the name of the ship in the ST stories I planned to write.
U.S.S. Challenger -because that was the original name of the ship when I got it and I liked it.
U.S.S. Valhalla -because my H.S. mascot was a viking.
U.S.S. Valkyrie -because that was the cheer squad at my H.S.
U.S.S. Andromeda -because it was my favorite ship in the anime series Starblazers.
U.S.S. Calisto -because for a Luna class, I like the name.
U.S.S. Capricorn -because it's my Zodiac sign.
I tend to use themes for an entire line of a toons ships. Irion's theme is warhorses so there's the Lipizzan, the Warhorse, the Percheron, and the Friesian. Plug's theme is cryptozoological primates because he looks like a cross between a orangutan and Big Foot's mini-me so there is the Wendigo, the Yeti, Yowie, Mogollon, and Nuk-luk. My science toon Baloo's theme is of course bears he still on the Miranda so it is called the Helarctos for the worlds smallest bear the sun bear.