Hunters and PVP.

They tear my mage(Brymstone- Blackhand) up, so I'm guessing that hunters are the mages counter in pvp?

Is this all hunters? Or just a particular spec or 2?

I've also noticed a few good ones have some sort of mod because they FD when I get the FoF proc causing me to lose target and often spend it on something else like his stupid snake trap.

What do you guys do against hunters, aside from bend over and grab the ankles?
You have to stay close to them, in all honestly you should attempt to LOS and use instant casts until you can get close enough to root them, Blink on their disengage etc. it's really weird at first to be thinking about it since we're usually kiting people and wanting to go away from them, but it's the opposite with hunters, you want to stay close to them.
poly-morph if he doesn't have someone dispelling him is important to close that distance gap when you first encounter him and also deep freeze, and your pets Freeze for shatters, basically outburst him but you have to do it at the right time.

You can assume that if you get up in their face they will disengage, so try to time your CoC just right so they waste it. Other than that, try to stay los or blink through him while he's casting steady shot and keep hitting him at melee range. Your shields come back and you have Evocation, he however, cannot heal himself. Be sure to use your Mage Ward to mitigate a few arcane shots as well.
The most popular pvp spec for hunters (Marksmenship) does counter mages pretty hard. However, it truly depends on the skill of the hunter as to whether or not you'll win the fight. A good hunter will all his CD's up will roll you over, especially if it's a skilled night elf, because they have a counter to everything we do. Blink? > disengage. DF -> trinket first/RoS second. Get to close? trapped. Pet nova - > deterrance/FD/Shadowmeld. Regular nova? Master's Call (freedom).

Plus you have to spend a ton of GCD's keeping your shields up through their ridiculous damage.

However, if you're fire and get a good combustion on the hunter before he deterrences, you'll win since he can't remove it in any manner. However, a good hunter will deny you your two novas with deterrence and master's call, so getting a fat pyro is hard to do.
Frost does well against average hunter's, fire does well too with some RNG luck and again an average hunter. Arcane is free Hk's (mana shield blow's and actually knocks the hunter back giving him space to gib the poor Arc mage, good one blizz). But a well geared and a well played hunter will almost always beat an equal mage, unless it's one of those godmode pro mages. No one beat's them:)
The only hunters I seem to have a problem with is BM. Pet damage is through the roof and I can't seem to get away long enough to evo and get some HP back.

I don't really have an issue with other hunters and if you do, just stand right on top of them. This will work (at least until MoP) and will drive them crazy. Save your blink for their disengage and /lol your way through their frustration. Depending on the grouping, if you're on the hunter the whole time and are not getting focused you will eventually wear down their HP.

I'd say keep dueling your fellow huntard friends.

PS. I play(ed) my huntard in pvp quite a bit and it frustrated me to no end that they can range me/insta-cast IL or CoC and I couldn't do anything.

Good luck!
You have to stay on top of them and spellsteal master's call as soon as they use it. Hunters have no self buffs so you will be able to get it on the first try every time if it's 1v1. The instant you spellsteal master's call, its game over for the hunter.

Remember to constantly root them and stand on top of them in melee range. Freecast shatter combos every single nova as they have no interrupts. Pet nova them out of camo and deep freeze every 20 secs. Their trinket is on a 2 min CD and our deep is only 20 secs.

Mirror image, invis, LoS/evocate, etc are also useful tools to defeat hunters.

The only time you should really lose to a hunter is when they are able to open on you from 40 yds away while you are attacking someone else. All of our roots will 'deathgrip' them back to us if you catch a disengage while the hunter is still mid-air and is one of the best counters a skilled mage has against hunters. This will let you save blink for an 'oh crap' moment.

Against BM hunters, use mirror image and iceblock to completely negate Bestial wrath. Sheep the pet after BW and counterspell the hunter, this will stop him from cleansing the sheep. Spellsteal a BM hunter's master call asap b/c it lasts longer than a Marksman's(and gives you a huge window of being unkitable).