Let's assume we can't count the Tardis for this category (maybe if there was a time and space category?). That leaves us with the Heart of Gold from HHGG, HMS Camden Lock from Hyperdrive, Thunderbird 3, the Altares from Day after Tomorrow, Interceptors from UFO, Eagle transporters in Space:1999, Red Dwarf itself or maybe the Bug. All of them are fun and interesting in their own way. But ..
Come on, it has to be the Liberator doesn't it?
It looks cool, it's the fastest thing around, it's got clever alien technology (including the always convenient teleporter), and it's the ship used by a bunch of plucky resistance fighters against an evil empire. The interiors may have been made out of Meccano and that stuff they use for sound-proofing recording studios but it's just a great ship. Who wouldn't want to find an abandoned alien spaceship that lets you be the cockiest pilot in the known universe? I loved the Liberator when I first watched Blake's 7 over 30 years ago. Opinions vary as to how well the show stands up today but they had a great spaceship. At least they did, until they blew it up!