Well, apart from anything I can design - 'cause I'm a writer and all - there is...
The TARDIS! - Well DUH! This should be mentioned more often, but I'm only the second, apparently.
The Post-Dated Check-Loan (Petey) - Someone did a Battleplate from Shlock Mercenary? Meet the giant vessel which makes Battleplates weep and...well...spoilers if you haven't read. Point is, Petey's awesome.
The Delphinus - The large experimental airship from Skies of Arcadia. Travels all over the world and can fight off world-destroying monsters.
A Reaper from Mass Effect - Let's just face it, it's a Cthulhu-ship and it lives in strange eons.
The Ki'tang Bird-of-Prey from STO - Specifically, mine. This is something I fell in love with while playing that game. It's an evil-looking vessel with a dark reflective hull coming out of nowhere and blasting shit to pieces. Named after the vessel of the Glorft from Megas XLR, the Karajor-Hydris is a devil of a machine and a fun ride, commanded by the biggest goddamn reptile you'll ever see in a captain's chair.