If you haven't already noticed, I don't really PvP. I'd like to get into more of the PvP scene, but for now most of these articles are going to be about raiding as a hunter. Please keep this in mind when reading this article. I'll try to dig something up on PvP gems at a later time.
So gems. Sounds pretty straight forward, right? 16 Agility gems are obviously best. Or is it 32 attack power? What about those pesky blue gems sockets, what do I put in there? And do I need hit gems? And what about..
Hunter's have quite a bit to think about when it come to gemming their gear. Luckily our friends over at Elitist Jerks have once again amassed a large amount of information about gemming for the different specs in their handy WotLK Gem Index. Again, there's a lot to read here, much like the rest of what Elitist Jerks puts together, so I'll give you a quick run down here. For more specific information about which gems are best in a given socket, check out the Index.
There are a lot of meta gems out there, but there is really only one viable choice for any hunter, regardless of spec and that's [Relentless Earthsiege Diamond]. Get it. Love it.
There's a lot of debate raging about what hunter's should use for their red gems. One side advises always using 16 agility gems, as agility gives AP as well as Crit, while the other side endorses 32 ap gems. So who's right.
Both. Or neither, depending on who the hunter is. Here's what EJ recommends:
Survival Hunters should go for the [Delicate Scarlet Ruby] (16 agility) gems. This is mainly because of the Survival Talent: Expose Weakness. This talent gives a 33/66/100% chance to increase your attack power by 25%. Pretty nice, right? Survival hunters also have several other talents that increase their agility by various percentages, so over all agility is always going to be the better choice for a survival hunter.
Beastmaster hunters should go for the [Bright Scarlet Ruby] (32 attack power) gems. There is an explanation on comment 11 of the Gem Index thread that elaborates more on the math of why this is, but for the sake of simplicity, here's what you need to know. Because of the way agility scales you get less critical strike from agility at 80 than you did at 70, where as Attack Power didn't scale in this way. 14 AP still equals 1 dps. Additionally, AP is the only stat we have that directly scales up pet damage, which of course is very important for a BM hunter.
Marksmanship hunters can go either way, though you'll see most hunters will advise you to gem up with agility gems anyway, simply because it makes switching back and forth between MM and Surv, which is quite common now with duel specs, more simple. Marksmanship hunters should use the WotLK DPS spreadsheet to help them decide which gems would be best with their current gear.
What if my gem socket isn't red?
Obviously not all of you gems sockets are going to be red, but I still recommend that for most cases you use whichever red gem suits your spec best regardless of the gem socket's color. There are several exceptions to this:
You're not hit capped:
Being hit capped is very important to hunters of any spec. Without talents or outside buffs(turn to your Draenei friend and give him a big hug) you need 8% or 263 hit. Obviously if you have Focused Aim or a Draenei in your group you'll need less than this, but that's a topic for another time.
If you have a yellow gem socket in your gear [Rigid Autumn's Glow] is going to be your best bet, especially if you need a lot of hit. Otherwise, put a red gem in it and ignore the socket bonus. Generally speaking the bonus isn't worth it anyway.
You need it to meet a meta gem meta requirement:
Obviously you're going to want to get a meta gem. As I recommended above, you should probably get [Relentless Earthsiege Diamond] which requires that you sport a Red, Yellow and Blue gem. The good news is you don't actually have to have one of each. A green gem, for example, will fulfill both the blue and yellow requirement. Depending on your spec there's a lot of green gems you could potentially pick to fulfill this requirement. Assuming you are hit capped, don't have mana issues and have a good amount of haste get a [Jagged Forest Emerald] regardless of your spec. If you are short of any of those three things pick a green gem that has whichever combination of the stats you are looking for. Check the Index to see the best options.
But what about Blue Gems?
Don't use use blue gems in PvE situations. If you need to fulfill a requirement that needs a blue gem, use a green. Otherwise, put a red gem in the socket.
Any discussion about gems could easily go on for days, but these basics should get you through most PvE gemming situations. For more details take a look at the Gem Index for yourself, and when in doubt, check the DPS spreadsheet!