Hunters are actually quite easy for just about any spec once you know the tricks. A large health buffer is especially helpful when you have a pet eating your face, but in general any spec mage has a good chance of getting up close and personal. Your general plan is to rush the hunter, depending on either Blazing Speed or your frost snares (depending on spec, or both if you're elementalist) while dishing out as much up close instant damage as possible. You're going to be casting very rarely, and even then only if you don't have the pet on you (or have Ice Barrier up, or Burning Soul). Stick to CoC, Fire Blast, FN + Ice Lance, etc. Even AE a few times to finish them if you have to.
So what can a hunter do against you? Let's find out.
Concussive Shot
Cooldown: 12 seconds
Duration: 4 seconds
This slows you to 50% speed, and with talents has a chance to stun. The only thing worth noting here is that once it wears off, you've got 8 seconds of totally free movement (assuming they don't wingclip). If you get stunned, it's generally a good idea to blink immediately.
Feign Death
Cooldown: 30 seconds
Most hunters will try to use this to avoid a cast time spell, especially while in a frost nova. This is a cooldown you want to keep track of, since if they've blown FD for any reason you'll have a better shot at completing a cast, especially if they've already blown Scatter Shot to try and get you in a trap. Speaking of which..
Freezing Trap
Cooldown: 30 seconds
This is your new target to use your trinket on, especially if you're a fire mage. Ice Block if you need to, but trinketing out of it will let you save Ice Block for a Bestial Wrath or Silencing Shot if you're desperate.
Scatter Shot
Cooldown: 30 seconds
Duration: 4 seconds
Range: 15 yards
Requires 21 points in Marksmanship
The classic Scatter Shot into Freezing Trap has been horrendously nerfed with the inclusion of the new PvP trinket that can break the freezing trap. This is another cooldown you want to keep track of, though generally you're not going to be casting much anyways now that the deadzone is gone. Mostly used to gain distance, try to Blink after a scatter rather than before it when possible.
Silencing Shot
Cooldown: 20 seconds
Duration: 3 seconds
Requires 41 points in Marksmanship
I personally haven't had much trouble against this ability, and I don't think there's much to say. Just rush at the hunter while you're silenced, and resume killing when it wears off. This is an ability that's nastier against healing classes, since hunters don't really have a spell interrupt otherwise, and you're not going to be casting anything besides a rank 1 frostbolt in range of this thing anyway.
Intimidation
Cooldown: 1 minute
Duration: 3 seconds
Requires 21 points in Beast Mastery
This actually triggers off the next hit of the pet, and is not an instant ability. This makes interrupting your casts iffy at best, and instead is generally used more as a general disruption tool. Smart BM hunters will save it for when you Blink, making you get stuck in the 3 second stun while they unload with Big Red (Bestial Wrath and The Beast Within) activated. If you know you're up against a BM hunter, try and force them to use Intimidation to keep you away instead, then Blink out of it.. They won't have Scatter Shot, so if you rush them and get close without blink they won't have many options to get away besides popping their big cooldowns (which we'll get to in a second). The animation for this is a little yellow fountain-ish thing over their pet, so if you see that while a pet is running at you, you can bet that you're about to be stunned. Anticipate it and get ready to Blink right out of it.
Bestial Wrath
Cooldown: 2 minutes
Duration: 18 seconds
Requires 31 points in Beast Mastery
The infamous "Big Red", this causes the hunter's pet to grow big and red (surprise), become totally immune to all forms of CC whatsoever, and cause 50% more damage.
Let's talk about how CC interacts with this ability for a moment. I've read a few mages saying that if you sheep the pet, the hunter can't activate Bestial Wrath. This is incorrect. As long as the hunter himself is not under any CC effect (such as polymorph), he can activate Bestial Wrath and any current CC on the pet will be broken. This is the hunter's ability, not the pet's ability. Don't bother sheeping the pet, especially with a BM hunter, as they'll just pop this to break the sheep on their pet. Between Intimidation, Feign Death, and The Beast Within, it's also almost universally not worth trying to sheep the hunter either.
When this ability is activated, don't panic. The pet will start to hurt, but if you stacked stamina (and you did stack stamina, right?), you can live through it. If you have Ice Block (and you do have Ice Block, right?), try to keep rushing the hunter for as long as possible. When the hunter does get range, then use Ice Block to wait out the rest of the duration. When it's all over, he should be cake to beat.
The Beast Within
Requires 41 points in Beast Mastery.
See above. All the same applies, as it's activated as a side effect to Bestial Wrath and not a separate ability.