From a hunter stand point, I would just drop a freezing or frost trap, concussive shot and just keep you at a distance.
From a rogues stand point i would use trinket, CoS, vanish, shadowstep, premediation, ambush, kidneyshot... do some dps... bye bye hunter (lol... not always). Dont worry about pet, I mostly ignore it.
The main concern when fighting hunter is to stay in close combat. Cripling poison is VERY helpful. When he manage to run out of your range, deadly throw can do a lot.
Just remember... STAY CLOSE... distant hunter = dead rogue :)
GL