Puzzle Quest: Galactrix features over 30 ships you can collect and customize. This guide will help you identify some general classes of ship and their most common uses. Since you can only have 3 ships in your fleet at any one time, it will also provide some suggestions for the best ships to keep.
Trident Battleship, Vortraag Destroyer, Trident Gunship, Vortraag Cruiser, Trident Warship
These ships have large reserves of Red Energy, useful for outfitting with lasers and missiles. They focus on directly damaging an opponent. It's always good to keep one of these heavy-hitting ships in your fleet for when you find that inevitable boss fight! Take care with some items like Mines and Minelayers though, because they can sometimes do as much harm as good.
Acheron Ghostship, MRI Blade, Cy-Tech Botship, Cy-Tech Needle
These are useful ships to have if you plan on spending a lot of time running away from encounters or smuggling contraband. Of course PSI Power will also let you escape your enemies so you may choose to concentrate on that instead. Keep in mind that many of the fast ships are also small, so you may be in trouble if you get caught. If you can manage to obtain an Acheron Ghostship though, you should be able to outfit it with quite a bit of equipment.
Lumina Archive, MRI Science Station, Lumina Warship, Lumina Cruiser
These ships have a large amount of Green Energy, representing the massive computer systems they have on board. Green Energy is useful for buffing your own ship, so Science vessels are often good defensive ships to keep around when fighting some big enemy capital ships. A science vessel with auto-repair functionality can last a very long time in combat.
Elysian Ferry, Jahrwoxi Homeship, Standard Hauler
If you want to make your fortune mining, then it is worthwhile to reserve one or more slots for these behemoths. Your cargo capacity is determined by adding together the capacity of each ship in your fleet, so it is never a waste to keep Cargo Ships around. Although these ships are not good in combat, they will save you the effort of constantly visiting distant stations to get the best prices for your cargo.
Long Range Ships
Cy-Tech Missile Array, Quesadan Lightship
These Ships have a high reserve of Yellow Energy. This is very useful for manipulating the board and can be a great way of denying a specific enemy the energy he needs to activate his most powerful items. In fact it is often worth keeping a long-range vessel and occasionally customizing it on the fly before a battle with a tricky opponent. Keep an eye out for Thrusters, Waves and Transformers that can be outfitted to these ships to target various gem types in play.
Lumina Archive, Trident Battleship, Gamma Sphere
These ships have 8 item slots and can be literally filled with all sorts of items. They are often slow, but also have good cargo capacity, so you probably want as many of these in your fleet as possible. However they are very expensive to buy, and even if you can find the plans it is very difficult to build one yourself!
MRI Mindship, All Soulless Ships,
These ships are obviously very versatile. Your biggest problem is locating one or finding all the cargo necessary to create one yourself.