Guardians of the Galaxy

Thanos is Mikey's older brother, Brand, from The Goonies

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Nebula is Amy Pond

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Ronan is Ned, from Pushing Daisies

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Yondu's lackey, Kraglin, is Kirk, from Gilmore Girls (he's also the brother of the director, James Gunn)

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Thor: The Dark World

Malekith the Accursed is the Ninth Doctor

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Iron Man 3

The Mandarin is Gandhi

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The Avengers

The Other (that dude who chills with Thanos) is Wesley Wyndam-Price, from Buffy

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Captain America: The First Avenger

Red Skull is Agent Smith

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Dr. Zola is Dobby

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Iron Man

Obadiah Stane is straight up The Dude

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