Transmute: Wild Jade

Note to those with [skill=755] who are searching for some information as I was about obtaining rare, MoP gems:

When [spell=31252], the best ore to receive rare, Mist of Pandaria gems is either Black Trillium Ore OR White Trillium Ore, with an average, gem, drop rate of 17% each (according to Wowhead).

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This ore can be obtained directly via two methods:

1. 
   
2. These can be mined from two, rare-node-spawns: [object=209313] or [object=209330].
3. 
   
4. If you are Revered with [faction=1272], plant [item=85215] for random chances at obtaining either type of Trillium Ore per plant.
5. 
   

This ore can be obtained indirectly by executing two steps:

1. 
   
2. If you are Revered with [faction=1272], plant [item=89233] to farm Mote of Harmony (yields 1 Mote per plant) and eventually make Spirit of Harmony to use as currency in the next step.
3. 
   
4. Purchase a stack of 5 Trillium Ore in exchange for 1 Spirit of Harmony.
5. 
   

Here is a quick list of each rare gem for easy-viewing:
Primordial Ruby
Vermilion Onyx
Sun's Radiance
Wild Jade
River's Heart
Imperial Amethyst

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Since Trillium nodes are rare spawns, a more surefire way to obtain rare, MoP gems is through [skill=171], specifically through Transmutations.
Being a Transmutation Master will result in the highest transmutation yields. Here is a quick list of each transmutation recipe for easy-viewing.

NOTE: Each recipe requires a Golden Lotus and the Uncommon version (listed below) of each, rare gem.

Tiger Opal
Lapis Lazuli
Sunstone
Roguestone
Pandarian Garnet
Alexandrite

Transmute: Primordial Ruby
Transmute: Imperial Amethyst
Transmute: Sun's Radiance
Transmute: Vermilion Onyx
Transmute: River's Heart
Transmute: Wild Jade

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If you DO decide to transmute and you are hard-up for Golden Lotus, you can:

      A) buy 2 in exchange for 1 Spirit of Harmony from NPCS:
            [npc=66685] (horde)
            [npc=66678] (alliance)

      B) become Revered with [faction=1272] to purchase, then plant:
            [item=85216] to get a rare chance at gathering a Golden Lotus
            [item=89233] to farm Mote of Harmony (yields 1 Mote per plant) and eventually make Spirit of Harmony to use as currency in option "A".

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LASTLY,

The least-effective way to farm rare, MoP gems is through prospecting:
Kyparite OR Ghost Iron Ore
Each having roughly a 5% rare-gem, drop rate (according to Wowhead).

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I hope this was helpful and saved you some time! Please feel free to add or suggest anything else!

So i made a bunch of gems:
I used the mats to make 1200 gems and transmutation mastery got me 232 extra gems. That is 19,33% extra gems.
I remind you, this may be far from the real percentage, as I may have been lucky / unlucky, but I hope this information may be useful nonetheless.