Herc II
Herc I
Ares
This is kind of a weird switch for me. First time I played through the main FS2 campaign, I loved the Ares (due to the sit back and blast everything to peices with trebuchets strategy).
But the next time through, on a higher difficulty level, I HATED the thing. So slow, so hard to maneuver. Yes, it can make a mess with a bank of tornadoes and a bank of trebs, but, in my point of view, a Herc II with Kayser/Subach (or Kayser/Maxim if you want to play with energy management), one bank of harpoons and one bank of trebs can do almost as much damage.
Ares has one shot to kill an opponent (unless using trebs), After that, a good pilot will leave it dead in space.
As for the Herc 1 versus Herc 2; Well, considering that I have terrible accuracy with primary weapons, having two extra primary gun mounts does me almost no good. Also, the Herc 2's second bay can carry 40 harpoons. The herc 1 can carry 48 total. Hmmm.
I fly the Herc II whenever possible, shield and engine power boosted slightly except for the end levels when you have the Kayser. If not that, then the Herc 1. And if I can't get either, I complain.