I wrote (sort of) in high school a story snippet about a large group of hapless wanderers in space aboard the Starship Zig-Zag.
Oddly, I wasn’t a stoner.
Jon the Intergalactic Gladiator flies into adventure in his trusty spaceplane the Danger Sled.
A sailing ship (Brig) in a short story set in the 17th century called Ma Coeur.
An independent, first in survey/scout ship in an SF universe novella called Van der Decken.
Sounds very Andromeda Ascendant, only more so.
Oddly, not very many of these come to mind, & I like naming things.
From my ideas for hard-science solar system exploration stories:
Sakerdess, inspired by a thread on this very board. Meant to be a corruption of sacerdos, & later a girl’s name.
Also, I wanted to write about astronauts using the hollowed-out asteroid 26734 TerryFarrell (what this says about me wanting to get into Terry Farrell, well…)
I’m sure I’ve come up with many others for stories I never wrote, or in games. I have come up with model or type names at various points, but that’s different.
Wow I thought for sure this thread would beabout the other kind of ships. Like Mulder/Scully and Kirk/Spock. 
I’ve been collecting cool names for characters/future children for years but I can’t find any examples of names for ships. Only two of my stories that I can think of even have ships in them, and I hadn’t come up with a name for either one yet.
I think my favorite fictional ship name from other people is the “Farrago” from Robotech: Sentinels, a slave ship of aliens literally pieced together from the various ships of each alien race enslaved on it.
Not writing per the OP, but when I TT-RPG’d, I had a Y-Wing fighter named The Meanstreak, inspired partially by the AC/DC song.
My wingman [del]Hero of the Rebellion[/del] partner in crime flew The Lucky Strike.
We are both WWII aircraft fans, and had appropriate “cheesecake” nose art picked out for our birds.
Ah! I forgot one I was going to mention, if no one minds my butting in again—
In a loose concept for a sci-fi setting, I dreamt up a mass driver “bomb ship” basically carved out of asteroid 216 Kleopatra.
It is/was to be named King Ludwig II. (Sister ships would include the Elagabalus, Tsar Peter III, and the Jean-Bedel Bokassa)
Naming ships like that…I guess like Ben + Jennifer = Bennifer, Mulder + Scully = Mully, Kirk + Spock = …:eek:
Baker and I wrote an agreeable naval yarn on these very boards that featured ships called Hector, Yarmouth, El Cordobes, Passamaquoddy, Leopard and Infanta Isabella (captured and renamed Gudrun in her role as a temporary “Swedish trader”).
Not a fictional ship as the OP requested, but for about three months I lived aboard a 26 foot sloop I named “Child O’ Fortune” in homage to Norman Spinrad’s book Child of Fortune.
I bought her for $600.00 and planned on fixing her up and sailing her all over the eastern seaboard and to the Carribean. Alas, she was a colossal piece of junk and ended up being scuttled and sold for scrap.
A while back I was working on a Star Trek Vs Star Wars fanfic in which Starfleet had assembled a battleship full of all the uber-tech ever come-across in the franchise: transwarp conduit/quantum slipstream consolidated drive, phased cloaking device, “batmobile” armor, quantum torpedoes, etc.
To be christened the USS Ultimatum…prototype registry NX-99000.
First in the Ultimatum Class starships, which include the USS Arizona, Bismark, Yamato, and Enterprise…USS-1701-F.
In one of the serial romances I wrote (shut up!) and shared with friends, the rich billionaire playboy had a yacht (natch) and, of course, he called it the Dionysus. Romances tend to go for the obvious.
In a story I wrote once there were a couple of boats named The Spanish Armada and The Not For Sale.
In a roleplaying campaign I ran there was a series of ships that were all named after people who got hosed in ancient mythology. The two the players dealt with were called The Iphigenia and The Philoctetes.
In a science fiction story I wrote, the ship was called The Spread Misere.
When I play NavyField, I name my submarines after stations on the Montreal Metro system.
Get it?
Surely an unparalleled adventure 
You were going well with the Ultimatum, but man… do you also have a Hood and a St. Istvan in that bunch…?
“Sir, there’s an enemy Raving Lunatic-Class attack platform approaching the outer defense perimeter”
An ocean liner named “Torpid Colossus” in a story to accompany a piece of artwork here.