This may be long, so bear with me - also, this is mostly aimed at PvE since I'm pretty much crap in any PvP setting that isn't standing back and shooting someone while they beat on Tormax:
Also, I haven't looked at Wowhead so I'm not sure what they have there. However, my take on things, which has often differed from other hunters in the guild (yeah I'm looking at you Nore).
Pre-3.0, yes, BM was the be all and end all of raiding. It was head and shoulders above both other specs, however, one SV hunter was nice to have because of the old expose weaknesses.
However, since the patch, things have sort of been shaken up and there hasn't yet been declared (at least in my mind) a "best" DPS spec confirmed. Also, depending on the number of hunters in a raid, it would probably be advantageous to have one of each spec (I'm thinking 25mans here) since each offer a buff that our raids (at least usually) don't have (i.e. an enhance shaman and ret pally).
In terms of gearing, it had always been straight up Agility, since agil offers not only AP, but also crit, dodge and armor with the kicker being that it all scaled with kings. With AP now scaling with TSA, AP gear is more useful than pre-3.0.
For raiding, my recommendation is to get as close to the hit cap (which is 264 without talents) as possible, then move to agility, followed by AP, crit, and intel. It's usually not as exclusive as that since most decent hunter gear will include a smattering of all of those stats with haste, and armor penetration also tossed in there.
For gearing you really just have to compare side by side two pieces of eq and take everything into consideration - there's lots of sidegrades or very slight upgrades around.
Pet Stats: your pet receives a portion of your stamina, AP, and hit (from what I know), and if your pet does spell based damage that is based off of your AP as well.
Shot Rotation: depends what spec you are. I'm not to sure what I'd do for SV (maybe ask Noreaga)
but for BM it's as simple as spamming steady shot, and popping BW whenever it is up. Don't bother with ANY other shots since they're not mana efficient enough to outweigh steady shot.
for MM, start the fight by popping all your +AP trinkets (once the tank has aggro of course) then serpent sting > chimera shot > steady > steady .....(till chimera is up)> chimera > steady > steady.....>chimera...etc.
This will give you the maximum DoT damage from serpent sting since chimera will refresh the initial value of the DoT that will be boosted from the trinkets. You'll also need to keep your hunters mark refreshed (every 2 minutes).
If you have kill shot, work that in when the boss is below 20%. Also at the start of the fight, thanks to readiness you can pop rapid fire twice at the beginning of the fight and maybe twice again later if the fight is long enough.
My post is sort of rambling since I keep remembering things and adding them onto the end. But I will say a good resource is the forums at
http://www.elitistjerks.com. Lots of people crunching the math that I don't want to bother with.
