So many choices, for many different reasons!
I love the Millenium Falcon, such a groundbreaking bit of production design - it's so rare to find something asymmetrical in Hollywood movies and I love it's grimy practicality. I love Firefly's Serenity in this way and for the same reasons, but I'd prefer something with a bit more fire-power if I had to choose.
I love the gothic grandeur of the Imperial Navy space-going cathedrals of 40K: Big, buttressed battering-rams covered in gargoyles and angel wings. Awesome! The nearest Hollywood got to that look-and-feel was the Cygnus in Disney's Black Hole - another favourite of mine.
I love the symbiotic biology of Moia in Farscape (I once even made a remote-control DRD for a convention). Also, a ship that can breed sounds like a great idea. Another organic ship that a lot of folk forget about is the LEXX. There's a lot wrong with LEXX as a ship (those food dispensers, ewwww), but anything that can blow up a planet is kinda awesome, too.
And last, but not least, the sheer model-builders delight of Space Battleship Yamoto: Love the idea of retrofitting a WW2 Battleship for space fun. I used to look out for old ship and 'plane Airfix model kits when I was a kid to bash them together into spaceships, long before I know Yamoto anime existed: It was like finding someone had shared the same childhood sci-fi fantasies.