It's like trying to decide between your children!
That was my first thought as well. It would be impossible for me to choose one single spaceship as my absolute favorite. So, proceeding with that thought in mind, in chronological order...

Earth vs. the Flying Saucers - the flying saucers (duh)
Doctor Who - the TARDIS
Lost In Space - the Jupiter 2
Star Trek TOS - the Enterprise; the Federation Shuttlecraft; the Klingon D-7; the Romulan Bird of Prey
Star Wars - the Millennium Falcon; Vader's TIE Advanced X-1; TIE Fighter; B-Wing; Star Destroyer; Tydirium Shuttle
Battlestar Galactica TOS - Cylon Raider
Star Trek Movies - Refit Enterprise; Klingon Bird of Prey; Klingon K'Tinga
Firefly - Serenity
Battlestar Galactica (New) - Galactica; Viper Mk II; "Razor" Cylon Raider

I'm sure there are others that aren't coming to mind at the moment, but that'll do for now.
 
For me it's.....

Starfury from Babylon 5
Bird of Prey, and Enterprise - E from Star Trek
T.A.R.D.I.S - Doctor Who
T.I.E. fighter (Empire) - Star Wars
Cylon Raider (Razor), Viper Mark II, and the Galactica - NuBSG.

But IF I had to pick just 1 it would be the Starfury!
 
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My all time favorite is the Enterprise from the TOS movies, that is such an elegant design and I never get tired of looking at it. Honorary mention goes to the Reliant and the Klingon Bird of Prey. My second favorite is the Space Battleship Yamato, nothing says cool quite like a literal battleship in space.

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Do I really need to answer this question?? lol

I will tell you my runner-up, and that is the ST TOS Romulan Bird of Prey.

The Wook
 
For me a tie between the ships Arcadia,Yamato,and the Macross SDF-1.

The Japanese know how to do ships!

Honorable mention goes to Star Wars,I love the old,used feel they have about like we're getting with planes.
 
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