Much like my preferences. Subach/Prom S for dogfight missions if Prometheus S is available, double Subach otherwise. Actually, in fighter combat the double Subach is nicer to use because of better rate of fire. If long range bomb interception is needed, Morning Star/Subach combo, same as with "disable stuff" -missions.
Secondaries depend a bit more on mission type. Bomber intercept calls for Trebs/Harpoons, Trebs/Tempests or Harpoons/Tempests combo, depending on what kind of range and what kind of ships are needed to be destroyed. Treb/Harpoon for missions where you need long range against bombers and mid-range accuracy against fighters, Treb/Tempest if you're up against heavy bombers and range varies, Harpoon/Tempest against light bombers when range is typically short.
Against asasult fighters such as Basilisks launching those thrice-damned swarm missile salvos on some hapless cruiser or freighter, double Hornets or Hornet/Tempest are fine.
Surgical strikes... either one bank of Stiletto II and one bank of something depending on opposition (Trebs if you need to also destroy bombers long range, Tempests if you need close range help in destroying turrets since Stilettos are overkill for them, Harpoons if you need generic aspect seekers), or dual Stilettos if you really need to destroy a lot of subsystems.
Surprisingly, Rockeyes can be used with relatively good success against turrets and stationary gun platforms, since they have longer range than Harpoons and you can use them to steal kills like in the first FS2 mission where you can rob the Belisarius kill to yourself by launching a salvo of Rockeyes on it...

They can also be used to lure the escort fighters away from those annoying cruisers in the third (iirc) mission (where you would be wise to question the wisdom of your leaders).