For me?

Flagship: The mothership from Independence Day, impenetrable shields, firepower to spare, planet destroying super weapons.

Cruiser: Asgard Cruiser from Stargate – SG1, Stealth, shields, and plenty of firepower.

Fighter: Defiant from Startrek DS9, stealth, shields, and overpowered weaponry.

One Flag Ship (a ship of any size that is your command ship)
A cruiser (any ship smaller than 2km)
A fighter (smaller than 40m)
Limit of one per universe