It's funny how everyone always waxes poetic about the ships being so balanced, and I even tend to be nostalgic about the incredible balanced combat system... but when I think about it... REALLY think about it... there were clearly some ships that destroyed and others that were pretty much useless in the heat of battle. I mean... a Supox or a Shofixti or a Zoq Fot would never be able to take down an Urquan Dreadnaught or the CHMMR Avatar.
Even your favorite Arilou would be pretty helpless against a Chmmr.
Other ships that weren't too useful... Druuge? Their "special" was burning up crew to accomplish something that other ships did automatically (recharge battery)? Same goes for the "special" Slylandro power (eat an asteroid) and the Pkunk power (insults) to recharge your battery - when other ships just recharge on their own? Kinda lame. Should have done something cool like charge up your main blaster or something.
Utwig's gun wasn't powerful enough... Shofixti had to die to do any sort of damage... Zoq Fot Pik's stinger was lame (should have been insta-kill if you managed to get that close)... I don't even remember what the Supox's special was... in fact, that race as a whole was nothing more than a sidekick, without any real plotlines of their own... Umgah and Thraddash just died far too quickly (with what, 6 crew??) to do any damage. Vuz was just a slow downgrade from the CHMMR.
As for the best ships?
I loved the speed and agility of the Pkunk - hardly did any damage, but their quickness made up for it and they ultimately could take down the Sa-Matra.
The Spathi ship was killer because it perfectly embodied the Spathi race. I'll never forget it. Squirt missiles out your butt as you're madly running away? Perfect strategy.
The Mycon was a very successful ship for me and did extreme damage up close and the cloud followed the enemy.
And I love... love love the Syreen's ability to make the enemy crew jump ship. If you can manage a battle stealing or killing crew on their way to your ship and when he's got just one crew left, nail him with your blaster? It's the ultimate Humiliation.
As for the BEST ships, the ones that were most powerful? It's an easy choice of three:
1) Chmmr Avatar
2) Urquan Dreadnaught
3) Kohr-Ah Marauder
Go head to head with any one of those, and you're probably toast no matter what. But this was probably by design - it wouldn't make much sense if the big-badguys were driving around a Stinger or a little Torch. They had to be awesome and tough!
Same goes for the CHMMR - arguably, most of the game is about setting them free - but if the ships you gained were the Yehat Terminator ships? Would be pretty anti-climactic.
And finally, my favorite ship, as well as the most powerful - a completed souped-up, decked-out Precursor Vessel. Heat-sinking blasters, 200 crew, never-ending battery, sides lined with turning jets and thrusters? Could take down 20 ships in a row, no problem. And I'm glad it ended up overpowered. I put 100 hours into the damn game, I better have a kickass ship by the end!