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Sigil of Wisdom has a small chance to "drop" for your character from LFR-difficulty raids, and only when the character is eligible to receive loot from the boss(es). Extra rolls have no effect on this.

This item drops when you are on the quest The Strength of One's Foes as part of the legendary gem quest chain.

The full quest chain for Chapter I is as follows:

It begins with the  Mysterious Note, which is given from several NPCs in Pandaria.  It will direct to you visit Wrathion in the Veiled Stair for the quest Stranger in a Strange Land.  Once there, he will ask you to share a drink with him for the quest A Legend in the Making which gives you some lore background and his story.

Wrathion will then give you two quests to complete:

• The Strength of One's Foes
• Trial of the Black Prince

 Sigil of Power and  Sigil of Wisdom drop in  Mogu'shan Vaults,  Heart of Fear, and  Terrace of Endless Spring on any difficulty level.

The reputation can be farmed from various level 90 mobs out in the world.

After this, you will get the quest Fear Itself which requires you to kill the Sha of Fear in the  Terrace of Endless Spring to get the  Chimera of Fear.  This item can be looted in LFR, Normal or Heroic modes.

Finally, he will ask you to meet just outside the inn to complete Breath of the Black Prince and pick up your new gem and the achievement  Chapter I: Trial of the Black Prince and begin the second chapter.

Sigils of Wisdom now has a small chance to drop in LFR Mogu'Shan Vaults, and Sigils of Power now only drop in Mogu'Shan Vaults. (Source)

Sigil of Power and Sigil of Wisdom as of Patch 5.4 now have a chance to drop from all bosses in  Throne of Thunder and from the first eight bosses (first and second wing) in  Siege of Orgrimmar if they are on the appropriate step of the legendary quest chain. It is also no longer possible for players to receive excess sigils.

The sigils cannot be earned from using a Bonus Roll.