The Tarsus is generally inferior in everything unless it is the Righteous Fire version where you can get decent shield and armor upgrades. It not only has the thinnest shields and armor in the game, but it is also the slowest ship. Upgrade to something else before taking on the main plot missions unless you like the extra challenge.
The Orion has decent speed and the heaviest shields armor in the game--you're more likely to have your external systems destroyed and want to reload your saved game anyway than you are to have your armor entirely destroyed. Its chief drawback in my opinion is that it is the only ship that cannot mount two missile launchers. That sucks because a salvo of two missiles can destroy anything lighter than a Dralthi--I like to use missiles to take out the first enemy quickly whenever I am outnumbered more than three to one. However, for somebody who prefers gun kills and wants protection and a low-cost ship, the Orion is a good choice.
The Galaxy is my personal favorite. It has everything better than the Tarsus--more speed, more shields and armor, more cargo space, and the top and bottom turrets. While it may be a little slower than the Orion and have less shields and armor, it makes up for that by having that all-important second missile launcher. It's fairly middle-of-the-road as a fighting craft (too bad the turrets don't auto-fire in Privateer!), but I love being able to tractor in the salvage after battling pirates and then sell it for cash!
The Centurion is the civilian counterpart to the Rapier--it sports two missile launchers, four guns, decent but not heavy shields and armor, and is quite fast. While some players prefer to use four of the same gun type for a massive volley (usually Tachyon or Particle cannons), I prefer to use one pair of fast-firing long range guns plus a second pair of heavy-hitting short range ones (such as Tachyon and Ion or Particle and Neutron). The Centurion is the ship of choice for the player who wants lots of attack power.
What I really think that Privateer should have had, though, is a light and fast fighter. Something that flies 600/1200 kps with better agility than the Centurion, level 3 shields but half the armor of the Centurion, no rear turret and 2 missile launchers/2 guns.