Runes that apply to Hunter pets:
Beast Mastery: Passive stats and a taunt. (Pretty much useless now, courtesy of nerfing it because it worked with Melee and MM hunters)
Flanking Strike (Only works in Melee…and is only there to make Melee stronger.)
Focus Fire: Non-Claw pets need not apply.
Cobra Strikes: Non-Claw Pets need not apply, and would’ve been great if Lion had started as a booked aspect so we could take it. Now we can use it just in time to lose kill command to use it with…
Now for the recommendations:
Beast Mastery Rune: As is is normally, but additional changes if Bestial Wrath is taken:
-Pet Health Increased by 25%
-Reduces Pet’s Bite Ability CD to 3 seconds.
Focus Fire Rune: Stacking speed buff last 16 seconds. (To allow BM bite pets the possibility of reaching 5 stacks.)
Kill Command: Bring it back and put it on the cloak. (Or put it back on the legs and let Kill shot go on the cloak.)
Trap Launcher: Also increases your pet’s damage to the targets you’ve trapped in the last 15 seconds. (Not useful against bosses, but plenty for open world and PvP)
These are all just off the cuff suggestions from my experience in BGs and Open world. I don’t raid on my Hunter. (Doesn’t seem BM has been welcome there for quite some time.)
I’ll edit it as better suggestions come along.