Heres my "little" summary of how I play against hunters.
First off, your voidwalker can taunt the pet off of you if the hunter is careless. I'm always amazed at how dumb most hunters are...well atleast the ones in my BG. Half their dmg is from their pet, and yet they dont even pay attention to what hes doing. If you do pull this off and the hunter hasnt noticed the switch, make sure to have your voidwalker attack the hunter instead of wasting its dmg to the pet.
I use Curse of Weakness on the pet as well as corruption for double the chance to proc nightfall. Make sure to get a good combat text addon for tracking nightfall procs. I use
Mike's Scrolling Battle Text mainly because it tells me in big purple letters on the top of my screen whenever nightfall procs. You dont want to miss out on a free shadowbolt cast because you didnt realize in time that you got the proc. It's also useful for alerting you when your health or mana starts to dip. Personally i find it harder to kill the pet than it is to just kill the hunter himself, especially if its a crab or anything like that, so I use Curse of Weakness to lower the dmg it deals to me.
Another useful tip is to sacrifice and immediately after cast drain life on the hunter. As long as your shield holds the channeled spell wont be cut short by dmg, giving you some much needed HP back. Using drain life whenever possible can keep your hp at a decent level, while the hunter's hp continues to decline. Note that you wont outheal his dps with drain life, so just standing there spamming it only succeeds in giving the hunter an advantage.
Get up in the hunter's grillz, if he wing clips you to run away ur in good position to get a fear off, and if he doesnt u can get behind him and melee him up as ur dots eat away at his health. Always make sure to right click on the hunter at the start of the battle to engage auto attack, so if he comes in for a wingclip or you catch up to him for a fear you can do an additional 50-80 free dmg (stalves hit for more than you might think =P). Dont be TOO worried about CC, but that doesnt mean ignore it - you are not a melee, you deal the same dmg at range as you do right in front/behind him, but the hunter DOES need to worry about range for his dmg output. Dont feel the need to trinket the first CC he puts on you, be it a web, concussive shot or wing clip, as if you do it sets him up to CC you later when you NEED to trinket it but cant. Also, if you're going for a fear, begin casting fear immediately after u finish casting the first one. This way, if it resists, misses or he trinkets it you are in a good position to recover. If it hits the hunter cleanly you can just cancel the cast and begin DPSing as usual. Dont expect fear to last the full duration - your dots should break it after about 4 seconds. You can try fearing the pet a few seconds after fearing the hunter since the first fear is going to break from dmg anyway, but pets have a nasty tendancy to resist fears.
Use LOS to your advantage whenever possible (the "terrain" in the middle of the field doesnt block LOS like it should so dont count on that). If he cant see you he can't dps you, while your dots still hit for the same whether or not you can see the hunter. Try things like running around a corner in the flag room and then just waiting behind the corner out of sight so that you are in a good position to strike when the hunter follows you there. The same principle applies to the relief/berserker huts. If the hunter pops AGM, try to LOS him as much and as quickly as possible. You wont be able to outdps his shield, so it's better for you to avoid taking dmg during that 20 seconds, since his AGM will protect him from your dmg either way. If you get away from the hunter but his pet is still on you, you can dps him down to either kill him or get the hunter to recall him. Always make sure your voidwalker stays on the hunter in these situations - he cant bandage because of your DOTs, but if he gets out of combat he can just eat to heal himself.
Remember that Curse of Agony (which has 12 ticks over 24 seconds) builds dmg as it nears its end, while Corruption (which has 5 ticks over 15 seconds) does the same dmg over its entire duration. From wowwiki, the first four ticks of COA combine to only ~1/6 (16.6%) of the total damage of the spell. The next four deal ~1/3 (33.3%), and the last four together deal ~1/2 (50%) of the spell's damage. So, the last 8 seconds of COA are crucial, because during that time period the spell deals as much dmg as it did during the first 16 seconds. If you think you might not be in LOS/range of the hunter for a few seconds or one of you is running away, wait until corruption ticks and immediately recast it on him as to not lose dmg from recasting Corruption as it's about to tick. However, dont recast COA (assuming it still has a decent duration left and isn't about to run out in a second) so that as many of its high dmg ticks are not wasted as possible.
Also note that Searing Pain and Immolate instantly deal dmg to the hunter upon casting (Immolate has a dot effect as well, but that's not what I meant), while Shadow Bolt deals damage only after it reaches the hunter a second or 2 later, depending on your range. This is important for 2 reasons. First, the additional time in between the cast and its dmg could be the difference between you defeating the hunter and living to continue towards your objective, and only defeating the hunter with DOT dmg after he already killed you. Second, if you are lucky enough to open on the hunter or the hunter temporarily loses track of you, Searing Pain or Immolate wont leave a trail leading the hunter back to you (he can tell the general direction a shadowbolt was cast on him from), which might give you a few extra seconds of free DPS.
[ITEM]4388[/ITEM] is sick against hunters (u dont even need to be an engineer to use it) to prevent him from outranging fears and etc. It also lowers his dmg delt by a nice little chunk, giving you a better chance to survive his dmg. This is best used after the hunter has already used his trinket on a fear, because if he trinkets something while this is on him this should be removed as well (including the dmg debuff).
When using lifeblood (assuming you have 225 herbalism, which you should), dont do it right as ur about to die - make sure to give yourself a little wiggle room. The actual healing doesnt start until 1 second after u cast it, so if ur at 50 hp and u cast it the hunter only needs 1 more hit on you. This goes for battling classes, not just hunters.
Against a geared/skilled hunter you're fighting an uphill battle, since he should have all the defensive cooldowns (except sacrifice) that you do in addition to more dmg. But that doesnt mean that it's unwinnable.
