Here are a few of the pets I use for certain situations:
Succubus (best for gaining honor, every tamer should work them every once in a while):
I use my cu. With self healing and damage which targets the succubi's weakest resists, the cu is the best option for gaining honor from succubi.
Thrasher: For gaining honor, the cu sidhe. For just killing it for ML marties, the rune beetle/bake kitsune combination
Miasma: Greater dragon. The rune beetle does well too, and kills the Miasmas faster, but the dragon requires less maintenance.
Bedlam (all creatures, hunting alone): Greater dragon. Not much else can take that much abuse.
Bedlam (Red Death): Cu sidhe. The Red Death is horribly weak to energy. With a cu sidhe and an undead slayer spellbook (I have EI rather than spellweaving), a Red Death dies before the cu is in trouble nearly all the time.
The Citadel (Key collecting): Any good pet combination works well. My favorite is the nightmare/rune beetle, but the greater dragon is probably better, assuming you can get it to the red key area.
SA mini spawns:
Any spawn with fire demons (there are three): Greater dragon. Being nearly immune to physical and fire damage helps, even though they kill more slowly than my favorite beetle/bake. A pair of bake kitsune are also very effective here.
Wyvern [reknowned]: Also greater dragon. Other pets are passable there, but since you can't use your vet skill against the forgotten servants due to their area effect attacks, you really want the higher resists of the dragon.
Cavern of Discarded: Are you daft? Use a warrior with a soul seeker! But if you are bored and want an easy spawn, take a pack of something or a rune beetle/something else combination. Otherwise the reknowned rats take too long to kill. (True story, I was working the spawn with my swordsman while two tamers were working with their dragons. I finished both before the two dragons were half done with one reknowned)
Goblin spawns: doesn't matter, they drop like mongbats anyway.
Undead spawn: I've only used my beetle/bake there. Others may or may not be better.
Acid spawn: Greater dragon. The acid attack from the interred grizzles do physical damage, making the dragon the best survivor there.
Navery Nighteyes: cu sidhe or beetle/bake
Medusa: either no pet or one greater dragon. Make sure you can kill the dragon quickly.