Gem itemization in Mists
In an effort to keep everyone from just stacking red gems in nearly every slot, Mists of Pandaria has changed gem itemization. Now gems give you either 160 agility, or 320 of a secondary stat. Hybrid gems (orange, purple, green) give you 80 agility and 160 of a secondary stat.
It's kind of like gluing a beard on an elf and cutting them off below the knees -- it makes them a lot more attractive, but still not the real thing.
This does however make hybrid gems often worth using in non-red slots, but not always. Like Cataclysm, agility reigns supreme and one point of agility is worth more than three times one point of a secondary stat.
Another interesting change with Mists gems is that epic-quality gems are only available as hybrid gems -- there is no epic red gem. This further pushes the desirability of hybrid gems in non-red slots, though not enough to make them always worth while.
Finally, it's worth noting that for rare gems (blue quality) we actually appear to have two versions of every gem: jewelcrafters cutting green-quality gems have a chance to proc a "perfect" version of the gem, which is then a blue gem with the same stats as the rare gem cuts. So be sure to check the prices of both on the AH before buying.
Agile Primal Diamond is the new hunter meta-socket gem, providing 216 agility and 3% increased critical strike damage. This is the single most important gem with the largest contribution to your DPS, and should be your top priority.
For red sockets the Delicate Primordial Ruby provides us with a straight 160 agility. This is the preferred gem for every red socket, even better than the epic hybrid gems. You should never have anything else in a red socket.
In yellow sockets we want to use either the Deadly Vermilion Onyx or the Perfect Deadly Tiger Opal, both of which provide 80 agility and 160 critical strike rating.
If your budget supports epic gems you want to use Deadly Sardonyx for your yellow sockets, providing 100 agility and 200 critical strike rating.
Blue sockets are the trickiest gem socket, and the best gem to use depends on the socket bonus for that piece of gear.
If the socket bonus is a secondary stat (hit, expertise, crit, haste, mastery) then you want to stick with the red Delicate Primordial Ruby and ignore the socket bonus. The DPS value of the secondary stats is simply not high enough to compensate for the lower agility.
However, if the socket bonus is agility, then it's worth going with a hybrid gem. You will want to use either the Glinting Imperial Amethyst or Perfect Glinting Roguestone, both of which provide 80 agility and 160 hit rating. If you've got the budget for the epic version, you can go with Glinting Zyanite that provides 100 agility and 200 hit rating.
The idea here is that you're going to be hit-capped with or without the gem via reforging, and using this gem lets you either not have to reforge out of another secondary stat, or allows you to reforge a lesser stat into a better one rather than into hit.
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