In my opinion these are the greatest Ships in Sci-Fi history.
1. The TARDIS, it's a blue police box that can travel anywhere in time and space, plus it's dimensionally transcendental. who wouldn't want one of these?(Doctor Who)
2. The Millennium Falcon, a highly modified CEC YT-1300 stock light freighter, piloted by Han Solo. In other words, not only the fastest hunk of junk in the Galaxy, but also the coolest! (Star Wars)
3. Serenity. Serenity is a 03-K64 Firefly-class mid-bulk cargo transport, serving as a home, transportation, and base of operations for Captain Malcolm Reynolds and his crew. I love this ship, I think the best word to describe it is character. (Firefly/Serenity)
4. Slave I. I have no clue why I love this ship, I just do, It maybe due to it's owners: Jango Fett & Boba Fett. (Star Wars)
5. Liberator, I loved Blake's 7 as a kid, and this ship design has always stuck in my mind. (Blake's 7)
6. Tantive IV, The Rebel Blockade Runner was the first starship I ever saw on screen as a child, this will always have a great sentimental hold on me (Star Wars)
7. Scimitar, Darth Maul's Sith Infiltrator, this may have only been on screen for a short few seconds, but I loved the clear foreshadowing of the design, and the feeling of darkside menace that it instilled. (Star Wars)
8. Klingon Bird-of-Prey. This is the only Star Trek craft to make it onto my favourites, as most are bland and uninteresting. (Star Trek)
9. J-type 327 Nubian royal starship. I have no other reason to love this ship, other than the fact that it is sleek and chrome, which would make it virtually invisible in space, and that it is based on the real worlds greatest ever aircraft designs, the Lockheed SR-71 "Blackbird" (Star Wars)
10. The White Star. Sleek and organic, also proves why in my opinion why Babylon 5 will always be superior science fiction to Star Trek. (Babylon 5).
I haven't included any Starfighters in this list, i'm saving them for another day.