I prefer the Athena over the Apollo or Herc; I've always loved it, despite the fact that it really isn't a bomber. It has all the hallmarks of an older prototype rushed out in haste to fight the Shivans, which explains its lack of actual bombing capability and terrible compatibility. That said, it turned out pretty good all things considered.
Ok, it's only got four guns, and the compatibility's pitiful, but the Avenger is more than sufficient for most uses (I actually greatly prefer it to the Prometheus). It's faster than the Herc, and has more missiles! And it's moderately tanky as well. If you think of it as a heavy assault fighter and missile boat (compare Herc-II), it's actually surprisingly good.
In terms of which one actually won the Great War, tho, I'd have to go with the Herc. Nothing against the Apollo, it's a surprisingly capable medium fighter given it's a tech-generation or so behind, but AI pilots survive longer in Hercs.