I came too late for 5000 range Tachyon Lance. I started on the last version before skills were added, and Tachyon Lance had 2500 range among other nerfs.
But... that reminds me of another absurd one: Unlimited Salamanders and Fast Missile Racks some time during the mid to late 0.6.x era. Stuff like Condor, Venture, and Doom (when it had Fast Missile Racks instead of Mine Strike) can spam unlimited Salamanders and kill everything from beyond fog-of-war. At first, Salamanders did 500 (frag) damage. Then it was toned down to 100 damage, but even nerfed, ships could still kill everything beyond fog-of-war. It took charges to Fast Missile Racks to end that game-breaker combo.
Others...
No CR and no peak performance before 0.6a.
All ballistics had ammo. A later 0.6.5 release gave them charges like autopulse. After that, ballistics became unlimited.
Maneuverability Jets (on Eagle and Conquest) kept their boosted top speed after the system ends as long as ship does not try to change velocity.
Vent cancelling on ships with Burn Drive.
Vent spamming.
Fading shots hit for hard flux beyond their listed range.
Fighters were treated as ships before 0.8.
Pre-0.7.2 Aurora was a better Gryphon than Gryphon, with large missile mount instead of medium synergy.
Gryphon on its debut release had Missile Autoforge that costs CR% to use, instead of one charge only. That version was used for that infamous pic of Reaper spam against Onslaught. Also, first release Gryphon had better stats, at least more OP.
Pre-0.8 Hammerhead was awful, with terrible stats, and Accelerated Ammo Feeder was suicidal back then, with no flux use discount to compensate for faster fire rate, meaning AI flux capped almost instantly.
Sparks in first 0.8 release had two burst PDs. Six on Astral can solo everything except the simulator (barely).
Phase cloak before 0.7.2 did not have time shaft, and did not have cooldown. It was basically a ghost variation of Fortress Shield.
Phase cloak before 0.9 had invulnerability frames. Afflictor (and other phase ships) can kill ships point-blank while decloaking and not take damage.
Pre-0.9 hyperspace storms were terrible, slowing your fleet to a crawl and gobbling up supplies. Good riddance.
Pre-0.9 light needler has 800 range. Not sure if lowered flux use will be enough to make it worth using over Railgun in 0.9.1.
Current, but soon to become the past once 0.9.1 breaks out: Perdition wings. Overpowered for their cost. Khopesh was nerfed in 0.9, only for equally priced Perdition to replace them seamlessly.
P.S. More...
Flux overcharge for energy weapons. Weapons on ship grew brighter and stronger the higher flux was. (Base stats of energy weapons were weaker, but their main advantage at the time was unlimited ammo, while ballistics had limited ammo.)
Hellbore fired twice as fast before 0.8. It was a top-tier weapon at bargain OP cost (and could be bought at Open Market). Ammo lasted longer than HAG while ballistics had ammo.