My favorite is the "Nostalgia for Infinity" from the Revelation Space novels. It's four kilometers long, but can be piloted by one person. This being a realistic series, it is a bit different from most examples: it can't reach or exceed the speed of light, but by accelerating for a long time it can come close. It's covered in a layer of ice to protect it from space debris, and has a hull made of "hyperdiamond." It lacks artificial gravity, but the thrust from acceleration causes a gravity-like effect; its hundreds of decks are laid out more like a skyscraper than a ship. The bridge is near the center of the ship, making it the least vulnerable part. It has weapons that can devastate cities from orbit, onboard factories that can create smaller spaceships, and a "warchive" that can recreate any weapon, ever. If you haven't read this series, you owe it to yourself to do so.
Other spaceships I like:
-The Bebop, Swordfish and Red Dragon
-Serenity and the Alliance ships
-The Outlaw Star, from the anime of the same name
-All of the Shivan ships from the Freespace games, but especially the Sathanas
-The A-wing, B-wing, Executor, Lambda Shuttle and Blockade Runner
-The Normandy SR-2
-The Planet Express ship and the Nimbus from Futurama
-The spaceship from the beginning of Avatar, another realistic example