My top 5.
1. Plasma Siege Starship (10 million health/ship, high burst damage and long range. Bye bye Force Fields and everything under them) - Counters: Engine Damage before it gets in range and manually targeting all Bombers, Starships and Needler Turrets to destroy it asap.
2. Armor Ship (30.800.000 cap health and bonus damage vs Structural and Turret) - Counters: Minefields, Bombers, Heavy Bomber and Plasma Siege Starships and Needler, Laser and Tractor or Gravitational Turrets protected by Force Fields.
3. Eye Bot (Invisibility, Immunities to Missiles, Sniper shots and FFs, Cloaking Booster, bonus damage vs Structural and Turret) - Counters: Tachyon Beams, Minefields, Laser and Lightning Turrets, Heavy Bomber Starships and Riots with Tractor Turrets.
4. Spire Stealth Battleship (Invisibility, 1,92 million health/ship, bonus damage vs Structural) - Counters: All "Ultra-Heavy destroying things" and Heavy Bomber and Plasma Siege Starships.
5. Space Plane (Invisible, fast, swarmer (kind of), Radar Dampening<Range, high dps, attack multipliers (all of them)) - Counters: Tachyon Beams, Minefields, Sniper Turrets and Missile Frigates.
EDIT: Other note worthy ships starting from the worst
-Leech Starship - Counters: Leech Starships of your own and manually targeting all "Heavy destroying things".
-Sniper/Sentinel Frigate - Counters: Snipers, Sentinels, Raptors, Space Planes, Raid Starships
-Zombard - Counters: Zombards, Raptors, Space Planes, Raid Starships
-Spider Guardian - Counters: Manually targeting Missile Frigates, Heavy Bomber and Plasma Siege Starships
-Munitions Booster - Counters: Manually targeting Missile Frigates
..so many nasty ships.... brb gonna list half of the ships soon
