Well, in a perfect raid setup you would still be expected to be MM, as survival might deal a percent more individual damage with adequete gear, but placing you in a group with 3 rogues and a fury warrior for Trueshot Aura will end up boosting the raid DPS by a lot more and it would benefit the entire raid far greater than the few extra percents of damage you would be pulling on your own. Hardcore endgame guilds usually don't want their hunters to go with survival because of this reason.
Also don't know how it's here, but on Warsong hunters still dealt more damage as MM even when in T3 gear when comparing to Survival (Yes I had all the best consumables and I was on the best available rotation when I tested it for myself - I'm a min-maxer, so I always conduct these experiments for the best available damage output).
If you manage to keep your pet alive at all times, then the best spec is actually 20 / 31 / 0 with Lupus or ZG raptor. Outperforms survival and regular MM. The pet does a considerable amount of damage. just have to keep an eye on it at all times.
Also other class/spec combos, which are a joke in raids are:
1) Assassination rogue - great burst damage for 20 seconds, but sustained damage is crap end up dealing 2x less damage than combat-swords rogues.
2) Feral druid, outperformed by every melee class in comparable gear in vanilla. 16 debuff slots kick the bleed effects out.
3) Subtetly rogue - some might argue that 1 sub rogue is ok, as hemo boosts raid melee damage, but it actually isn't noticable and having a combat-swords rogue comes out roughly the same if you look at the raid DPS.
4) Ret paladins - are a joke, but a geared & skilled ret paladin can actually deal decent damage in naxx for the lols due to the undead nature of the instance, but he has to make sure he stays on adequete mana levels and spams all consumables (Watch youtube videos), but you would still be better off with a geared mage/lock/fury when talking naxx gear.
5) Prot paladins - useless in vanilla, they can manage to tank patchwerk for the lols due to the undead nature of Naxxramas, but a warrior can still do a better job (watch youtube videos)
6) Enchancement shamans - Their DPS sucks, the totems buffs provided to other melees aren't worth the DPS lost on the individual shaman. Some might argue that having one with nightfall would boost DPS, but in reality the 16 debuff slots and nightfall not procing as much on a fixed server kills the boost, better to just have another awesome DPSer
7) Elemental shamans - still suck compared to a warlock/mage and go OOM fast, no sustained DPS
8) Demo locks - in theory manage to pull decent DPS, but still crappier than having an awesome destro lock
9) Balance druids - go OOM in 45 seconds
10) Fire mages in MC/BWL - mobs have great fire resistance levels
11) Arms warriors - Back in vanilla when theorycrafting wasn't popular it was believed that having one in raid is ok, but his DPS still sucks compared to having a decent fury or another good DPS class.
12) BM hunters - hunters didn't really excel when it came to dealing damage anyway. I mean a skilled hunter could pull decent DPS, but a mage/warlock/fury of comparable skill level would still easily outperform a hunter. The grim truth is that hunters were mostly only taken along for tranq shot / kiting / pulling to tank purposes. And they were always placed in melee DPS groups for Trueshot aura to make some extra use of them.
13) affliction locks - might have been ok at MC level, but a destro lock or SM/ruin could still outperform an affliction lock.
That's all that comes to mind right now.
Unfortunately it's pretty linear, key player classes in ~Naxx gear are:
1) Warlocks (greatest potential damage output)
2) Mages (2nd closest)
3) Furys in adequete gear (easily outperfrom rogues in comparable gear once in Naxx)
These 3 classes are the core DPSers, I'd go as far to say that having your raid consist only of the first 2 would maximise raid damage and give the best peroformance overall.
4) Prot warriors for tanking
5) Holy/disc priests
6) Holy paladins / resto shamans
7) Resto druids
8) minimum amount of MM hunters necessary for an encounter
9) minimum amount of combat rogues necassary for an encounter (combat rogues were comparable to fury damage up until BWL , but after around AQ40 a skilled fury can outperform a rogue of equal skill & gear, gets even worse at naxx levels.)
This is your perfect raid setup unfortunately, so it does get a bit dull and linear in vanilla. In a perfect raid your damagedealers would consist only of mages & warlocks to maximise damage output
