Fighters can handle any job, except possibly shielded Remnant battlestation fights, if you bring enough of them.
Thunders have the best offense of 8 (or less) OP fighters, but the wing is fragile as a whole because of long replacement times. They can hit any defense and they can lockdown ships (though Claws are better at the lockdown job). Thunders probably want maxed-out carrier skills (and definitely Expanded Deck Crew on the mothership) to do well, although Wing Commander 1 might make them too fast to use their weapons very well. If you want to use Thunders for long-range assault, it is best to stack as many as possible. (I usually use Thunders as a Claw substitute if I lack the latter. If I want to kill things, I bring Warthogs.)