Monkeys are ugly. Moths are beautiful.
As a BM hunter, to BG's I always bring Moth & Wolf, and keep out Moth pretty much 99% of the time. I've never been in an instance where I wish I had a monkey, bop, or bat in a bg, so giving my party a fat buff when I can then switching back to moth the rest of the time does just fine. Against match-ups moth isn't effective against intimidation, post-haste disengage, concussive shot, scatter shot... usually are effective. As for moths missing, if you really want an ez-mode stun, go with bat.
Spider would be a 2nd pet worth considering, I'd say... moreso than bops, possibly mores than monkey. Moth/Spider covers some good play. Spiders face roll melee classes, are great for peeling ppl off your flag carrier (2 at a time with intimidation!) and work great with the mobility you get from posthaste disengage. It's a good choice for hunters that find themselves in the position of flag carrier a lot, which is any objective player that pugs.
As BM, for BG's, I have to go with
Moth/Wolf
or
Moth/Spider
Bat/Wolf, Bat/Spider if you really need a universal stun on top of intimidation. Monkey, being that it's .5 sec cast and breaks on damage, is going to be even more situational than a moth when pugging.
edit: I think it really depends on what your spec is, too. If you're not BM, I would never recommend a moth. Then again, I wouldn't recommend monkey either... probably a bat if you really wanted a stun.
re: Lil's post on bops, I think as a purely anti-rogue fc-protection pet on MM bops seem good, but I usually see rogues struggle with spiders just as much, as it doesn't take the duration of a disarm to nullify the threat of rogues