For longer than there have been real spaceships, there have been imagined ones. Lucien of Greece used an actual sailing ship (caught in a whirlwind) for the first science fiction story around A.D. 120. Jules Verne used a giant cannon with a shell-shaped spaceship. (It's too bad no one could have survived the launch, but the SpaceX Dragon capsules remind me a bit of the shape.) As we moved into the 20th century, though, science started informing science fiction. And the results were often really cool.
My Top 5 ships from fiction
1. The obvious - the U.S.S. Enterprise. A lot of thought went into what may have been the first non-aerodynamic ship in film/TV SF history: that is, none of the fins and wings of Buck Rogers and his ilk. Gene Roddenberry and Matt Jeffries were not engineers, but they did a good job of working out a practical bridge and building outward from there. They borrowed the front section shape from (really) the coil on an electric stove. But it worked. (I do wonder if the bridge might be better on some projection from the saucer for an ever greater field of view...hmmm.) And just for fun: Could we build it for real?
2. The Nostromo from Alien. Finding this article is what got me thinking here. The Nostromo had clearly seen heavy use: it gave the impression of being a beat-to-hell ship that didn't have many years of service left. The article has designer Ron Cobb explaining how he came up with the freighter.
3. The Eagles from the otherwise forgettable series Space: 1999. I always thought the modular ships with detachable command sections and fuselage/cargo containers (a bit like Skycrane helicopters and their detachable cargo pods) were superbly utilitarian. The reason we don't use such low-slung ships in our lunar concepts is that the low gravity makes the "wedding cake" lunar lander design workable, but I think once we get to moving substantial loads around the moon (whenever that happens) we might very well go to something more like the Eagles.
4. The military landers from Aliens. Technically, they are UD64 Cheyenne dropships. They have cool ramps and armored personnel carriers, they are armed to the teeth, and to an ex-Air Force officer and longtime space aficionado/historian like me, they just look right.
5. The Valley Forge from the movie Silent Running. It was original, believable, and had forests on board. The original was crafted of parts from 800 model kits and was 8 meters long. Alas, it no longer exists. But it had forests. Enough said.
You'll note I avoided CGI spaceships, as good as many of them are. All these were done, in their original incarnations, with models. Because believable, highly detailed spaceship models are also cool. (OK, I've seen the original Enterprise, and it wasn't very detailed. But it was a breakthrough design, and it was a ship I'd like to serve on. As long as there was no red shirt involved.)