Another one:
The Going Under The Water Safely Device
Ha! I just re-read Jingo. 
From the Ringworld books.
HMS Atropos is specifically from Hornblower and the Atropos. 
Is C-57D from Forbidden Planet?
Time for hints:
Fin of God
Immer Essen (hint: Steve Martin)
Arabella
USNC Iroquois
Guinevere One
Tarantula (hint: operetta)
Splendor Hyaline (hint: seven-book series)
The Slippery Pig (hint: video game)
R-XM (hint: was on MST3K)
Icarus (hint: the Statue of Liberty)
Boise
USS Montana (hint: the Reds don’t have anything that fast)
The Moldy Crow (hint: video game)
The Betty (hint: Michael Wincott and Ron Perlman)
USS Orlando (hint: it’s a submarine)
Valley Forge (hint: Freeman Lowell)
Asgard
USS Kiwi
CosmoStrator (hint: was on MST3K)
HMS Indomitable (hint: the ship is sometimes called the Bellipotent because its editor was asleep at the switch)
Bosda’s picks:
Hispaniola
USS Orlando - Up Periscope!
USS Kiwi - Wackiest Ship In The Army
Icarus - Planet of the Apes
Valley Forge - Silent Running
There are still my additions as well:
Vrolijkheid
Sea Tiger
Tarantula----Spacecraft, Proxima Military TTA Handbook Spacecraft 200-2100
The Betty----Spacecraft, “Pirate Ship” Alien Resurrection
Hispaniola----Sailing Ship, Treasure Island
:smack: Planet of the Apes! (Starship, of course.)
USS Montana----Submarine, The Abyss
Valley Forge----Spacecraft, Silent Running
The ship that accidentally sailed too close to an island, and whose passengers were being killed off in Dead Men Don’t Wear Plaid.
Looking back, I see a hint. I didn’t need it.
Valley Forge is also one of the ships in the book Straship Troopers, along with the already identified Rodger Young.
Nitpick: Minnow was a private vessel, not a U.S. Navy asset, so her designation was “SS,” not “USS.”
My contributions:
Castle Wulfenbach
Not For Hire
Sleuth
It’s the airship from Girl Genius. Not just a name, either…it’s really a flying castle.
Which is why I wasn’t sure whether to italicize it.
For your further trivia pleasure, check out Name That Fictional Fiction. 
Not For Hire - The Fabulous Riverboat
Arabella - Captain Peter Blood’s ship.
Cosmostrator - First Spaceship on Venus (1962)
RX-M is from Rocketship X-M
My contribution is the Karnak
*Spindrift *is cheating. It wasn’t a starship, just a sub-orbital airliner.