choice 1 - TARDIS because it has infinite size and is powered by a suspended supernova
choice 2 - Covenant Flagship Master chief stole just after he left the first Halo Installation - It has the plasma beams that "Cut through steel like butter" along with dozens of Plasma cannons
choice 3 - Hyperion Flagship - Starcraft 2 - The Yomato cannon is gangster - Has a nice fold space jump to keep on the move as well
Edit: This was my choice one, but has since been moved to support:
Support Station - A maxed Vasari Rebel space station from Sins of a Solar Empire - It is capable of equipping many, many, many guns - it also has warp capabilities, provisions to house a full hangar, able to control a population remotely
English
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Choice one is the correct choice. Except it's a space station and not a ship... But it's still one of the best ones.