The USS Abraham Lincoln was the frigate that Professor Aronnax left Brooklyn on to kill the supposed animal that had been disrupting shipping, only to find out later that it was in fact the Nautilus which was the culprit.
Nobody going for the USCGC Eagle? (Clue - see an entirely separate threat that appeared today!)
How about a group of three together: the Yokohama, the Bahrain, and the Buenos Aires?
The various Skylarks - E. E. Smith
USCGC Eagle - S. M. Sterling’s **Islands ** trilogy
Snoopy - Lander for Apollo 10
Boise - E. E. Smith’s Lensman series, thundering through space with its inertialess drive!
Well, turns out we’re BOTH right. The Abraham Lincoln WAS Pinkerton’s ship in “Madama Butterfly.”
http://www.music.indiana.edu/publicity/opera/2006-2007season/internal/butterfly/synopsis.html
Moonlanding deniers? Otherwise I’m pretty sure the Apollo 10 lander was a real ship
I deny that Apollo 10 landed on the moon.
And there is a USCGC Eagle. I went down to New London and had a tour a few weeks ago.
HMS Indomitable - Melville’s Billy Budd (needed the clue)
Naglfar - The ship of the giants in Norse mythology
A hint for my choice (Vrolijkheid): If you got the Sea Tiger, you’re closer than you think, you filthy beast.
Skylark–e.e. doc smith’s Family D’Alembert series, starship
New York–Cities In Flight, starship and The City Of New York
Eagle–Apollo 11 & Space:1999, Starship
Snoopy–Apollo spacecraft, Orbiter
Just to toss in a couple more:
Fearless and Nike
Dahak
A very random one…
The Arcus Prima
Those are the 3 starships that the colonists used to get to Pern in Dragonsdawn.
The Epoch - Time traveling ship from Chrono Trigger
The Cherub (one of Carlotti Motors’ Angel series).
Sorry - I cheated and dug out the book 
. Haven’t read it in years - I might skim through it again for old times sake. Very soothing!
Here’s mine:
Arctic Warrior
The Louisa
USS Cygnus
USS Reuben James*
U-96**
Special question: in which movie does the QEII (playing herself) come under a particularly ineffective attack? (The real QEII is shown in an earlier establishing shot, but for the actual attack scene, I’m pretty sure they just used some soundstage trickery!)
- A real ship, who played herself, with the assistance of a similar vessel, whose real name is partially visible in one shot. The basic question is to name the movie, but a trivia nut would also hunt down the name of the second ship used to play the Reuben James.
** A real boat and the inspiration for a movie, which I don’t think ever mentioned the boat by that name or any other – so this is one where you name the movie and the boat’s movie name, if it had one.
Flinx’s ship from the Flinx series.
Two of Honor Harrington’s ships.
The Moon. Yes, it’s a ship.
Some from me :
Sideways Traveller
The Cloak of Untrammeled Dignity
Krashnark : Bonus points if you get what the name references.
Swampscott “the oddness that was the Swampscott”
Sea Sprite
Qin Shihuangdi
Rhabwar
The Cornucopia of Goods at Excellent Prices
Trihs, we have to get together sometime and talk SF!
The Cornucopia of Goods at Excellent Prices - Haviland Tuf’s original ship in G.R.R. Martin’s Tuf Voyaging
Swampscott - From Bunch & Cole’s Sten series, specifically Fleet of the Damned.
Since no one else seems to have got mine- or put them in any list- I’ll post them again with some hints:
The Proud Anselmo (hint: online cartoon)
SS Ssssss (hint: cartoon)
The Big-Ass Spanish Boat (like I said, this might be cheating. This came from a newspaper article which was plagarized from a humor website. Does anyone else remember this controversy?)
And some new ones:
Corvair
Leakin’ Lena
Venture (two possible answers- one is a tribute to the other)
Venture: ship in King Kong (also makes a cameo in Sky Captain & the World of Tomorrow)
Brian
OK, then, make that two tributes.
The Leakin’ Lena is from “Beany and Cecil”