Going back a ways, some other favorites:
Streaker, the ship crewed by a combined human and dolphin crew, from one of my all-time favorite books, Startide Rising.
Rama, from Arthur C Clarke’s Rendezvous with Rama, the mysterious cylindrical world where everything comes in threes.
The “Okie” cities from James Blish’s Cities in Flight, which travel the galaxy using the spindizzy gravitational control technology.
The Gaea torus habitat ship from John Varley’s Titan, which is a weird, wild, almost psychedelic SF fantasy.
An early sentient ship, Helva, from The Ship Who Sang by Anne McCaffrey.
And not a spaceship at all, but the whaleship Rorqual Maru from The Godwhale by T. j. Bass, an obscure favorite.
