USS Voyager, NCC-74656 will always be top of my list. Seeing her in S3 of Picard made me even happier than seeing the Enterprise D (though hearing Majel Barrett as the computer again was another favourite moment).
The SSV Normandy from Mass Effect (either the SR1 or the SR2 — they're both beautiful galaxy-saving vessels).
The Ebon Hawk from Knights of the Old Republic, even if it is an unoriginal design for the franchise.
Shawdow194