USS Expedient Pain.  
 
Favorite I saw in a short time playing was the USS Bubbles. Made me giggle.

U.S.S. Siren
 
(Joke) U.S.S. R.
 
Speaking of which, is there a Giantbomb fleet?

I'm not in the beta, but I'd name it the "U.S.S Triangle", after Asteroids. 

U.S.S Oscar Mike, I can't believe it wasn't taken yet.

Mine is U.S.S ZZZWWOOOOOSSSHSHHH

USS Giant Ship

Not that I'm going to play this but I would have to go with SERENITY

" Not that I'm going to play this but I would have to go with SERENITY "

USS Barnstormer & IKS Falconhoof
 
Both exist because the names make me laugh.

How does one go about joining the Giantbomb Guild/Clan/Fleet?

well when I finally get time to dl the beta it is going to be called the U.S.S Enora

U.S.S. MIMI

U.S.S Tieght Sphilnktor

U.S.S G-Funk

USS Prolapse 
add me bombers! 
Pvt. Prolapse@adamfedoruk

" USS Prolapse add me bombers! Pvt. Prolapse@adamfedoruk "

" @Coombs said:

" Not that I'm going to play this but I would have to go with SERENITY "

Excellent choice, that was one of the names going through my head while deciding the name  Awesome name for just about anything "

" How does one go about joining the Giantbomb Guild/Clan/Fleet? "

" @Venatio said:

" @Coombs said:

" Not that I'm going to play this but I would have to go with SERENITY "

Excellent choice, that was one of the names going through my head while deciding the name  Awesome name for just about anything "

lol wasn't that one of the choices for the name of that satellite Steven Colbert wanted named after him?   "

" U.S.S. U.U.C.C.K.K. "

U.S.S. Pwnage

U.S.S. Seeker of Truth. If you've played Persona 3, you would know where that name came from.

I'm on the U.S.S. Edison.
 
My next one will be the either the U.S.S. Tesla Or the  U.S.S. Archimedes.

U.S.S. H.M.S. Pinafore

Phew, just started playing.
 
U.S.S. Kittyhawk.

U.S.S. Alysium, piloted by Constantine Xavier Capernicus

Something Scottish...I was thinking:
 
USS Bearded Clam

U.S.S FutureLucha

I didn't bother with a cool name for the beta. You get proper ships once the full game is out. Cruiser class for me. :D

U.S.S. Unreliable

Captain That Yellow Bastoid of the U.S.S. Cheese Doodle 
 and 
Captain "dont remember name" of U.S.S. Funhouse

" Captain That Yellow Bastoid of the U.S.S. Cheese Doodle  and Captain "dont remember name" of U.S.S. Funhouse "

If I join it would be the USS Sir Mix-A-Lot. Hopefully by the 24th century, his contributions to mankind will be recognized.

" If I join it would be the USS Sir Mix-A-Lot. Hopefully by the 24th century, his contributions to mankind will be recognized. "

U.S.S. Red Dwarf

USS Exploder

Originally, it was the USS Pandora... Then I realized that people would think I was ripping off Avatar, so I made a new one. Damn you, James Cameron. Damn you and your crazy blue cat people!

The U.S.S. Ragnarok and the U.S.S. Armageddon are my two ships.
 
The best that I've seen so far in the beta, though, was Captain Zoidberg of the U.S.S. Planet Express
 
Edit: 1000 posts, didn't really put it to good use...

I like the word Maelstromme.

USS Bootylicious

probably go with USS MrSpaceship

USS Diddy Kong

U.S.S. Sunshine Rainbow