Common Best Comps for Hunters:
2's
1. Hunter / Shaman
2. Hunter / Paladin
3. Hunter / Priest
4. Hunter / Druid
3's
1. Hunter / Paladin (Holy or Retribution) / Shaman
2. Hunter / Paladin / Death Knight
As you can see in 2's, Hunters need healers to be good. Unfortunately my only serious 2's partner is a Rogue, so we just have to make due with an 1800-1900 rating. We got up to an 1880's rating before falling back to an 1818 rating. If we manage our CC flawlessly and play perfectly we have a chance to beat most teams. Unfortunately we do make mistakes and one mistake will cost you the game when your playing a bad comp.
Spell Penetration
Most top Hunters use 75 Spell Penetration to combat enemy fire resistance.
35 Spell Penetration Enchant on Cloak and two 20 Spell Penetration Blue Gems.
Specs
There is no exact cookie cutter spec that is dominating the charts for Hunters. Every top Hunter is a Survival spec, but each one specs a bit differently. Perhaps specs vary because there are so many mediocre talents in the Survival tree.
Hunter / Healer Spec
This spec is very similar to the specs of most top Hunters. I tend to favor Improved Concussive Shot, and could not see myself without it.
Double DPS Spec
This spec is a lot different than most top Hunter specs. This is partly because there is no top Hunter that is running Double DPS (to my knowledge).
Mana is not an issue since fights are short. Talents that benefit Frost Trap are not important because I will mainly use Scatter Shot / Freezing Arrow. Extra Hit chance is important to combat Rogues (4% miss chance from talents, 2% miss chance if Night Elves).
Rogue / Hunter Strategy
Our strategy revolves around our ability to perfectly CC one of their players. Ideally this is our CC rotation on easiest to CC target:
Sap (10 seconds)
Scatter Shot / Freezing Arrow (14 seconds)
Blind (10 seconds)
Vanish / Sap (10 seconds)
Scatter Shot / Freezing Arrow (14 seconds)
Wyvern Sting (10 seconds)
Cheap Shot / Kidney Shot (10 seconds)
That is 78 seconds of CC, however, this is not how things usually happen.
Real World CC rotation:
Other team manages to get in combat or has ground aoe to thwart off Sap.
Scatter Shot / Freezing Arrow (1-6 seconds as enemy will usually use their trinket)
Blind (10 seconds)
Wyvern Sting (10 seconds)
If my Rogue is quick on the blind that is a little over 20 seconds of CC. This should give us enough time to burst the other person down. If not, than my Rogue will go back to stunning up the CC target. But if we haven't killed someone 30 seconds into the fight, most likely one of us is about dead.
Ideally we could just CC their DPS and go all out on their healer. But we come across many Double DPS teams at our rating and a lot of Rogue / Healer teams (Rogues are very tough to CC).
Against any Holy Paladin team we have to go for the Paladin (as we cannot CC him through a Bubble) and CC his partner.
Pets
Tenacity pets are used when playing with a Healer. Roar of Sacrifice and Intervene are just too good in longer fights. Crabs and Turtles are the most common choices.
Ferocity pets are good for Double DPS. They bring more damage, instant rez and Call of the Wild. Wasps are the trademark pet for Double DPS as they bring Faerie Fire to the table, which screws up Rogues and Mages and thier ability to vanish / invis.