1. The Guardian of Orion (MOO1/2) - Alright, so MOO's a strategy game, but nothing beats an ancient autmated capship with blackhole generators, aptly named death rays, etc.
2. Hiigaran Battlecruiser (HW2) - Quad ion cannon arrays with point defense pulsar guns, a fighterbay, tactical FTL jumps, cloak field and gravity well generators, what isn't there to like?
3. Dreadnought class corvette (I-War) - Manuverable, interesting shield mechanics, able to engage forward and rear targets at the same time.
4. Waterloo class cruiser (WC2) - There's nothing like seeing capship v.s. capship warfare in an old sprite-based game.
5. Deimos class corvette (FS2) - Yes it's a brick, but it is a very functional ship that can hold its own.