Hunters are shaping up to be excellent in PvP this patch. We've always been sort of acceptable at very high skill levels, but now we have a bunch of new tricks in our toolbox. It's still too early to give a definitive guide to the best choices you can make, but with everything that's changed, it's worth going over where we are now.
Beastmastery is the spec of choice
Marksmanship was the most commonly played spec for the last two expansions, mostly because of readiness and silencing shot. These can now be learned by any spec, and since BM has the best damage of the three specs, it's the default PvP spec. In addition to the raw damage, BM also has an additional crowd control breaking effect with The Beast Within, a stun, and the ability to tame exotic pets, including one with a heal. On its own, that heal isn't much to write home about, but with glyphed Stampede, it can heal for a large portion of your health.