if judging by the outside the Agent's ship followed by the sith ship, then the smuggler ship, then the trooper ship and lastly the Jedi ship.
If judging by the interior as well, the Sith Ship, then the Agents' ship, the Smuggler ship, the Jedi ship, and Finally the Trooper ship.
If Judging by how they fare in combat, because I have noticed a difference, the Sith Ship then the Agent's/Trooper's ship, the smuggler's ship, and finally the Jedi ship.
I haven't done the Bounty Hunter yet, so can't really judge it.
Just got Bounty Hunter ship, worst exterior and joint worst interior, but the handling in space missions is equal to the Sith ship.