From Indiewire, the list of those that probably should have scored a nomination across a range of categories.

Best Director - Bennett Miller - “Moneyball”
Best Director - Rupert Wyatt - “Rise of the Planet of the Apes
Best Score - Alberto Iglesias - “The Skin I Live In
Best Cinematography - Sean Bobbit - “Shame”
Best Cinematography - Robert Elswit - “Mission Impossible: Ghost Protocol”
Best Art Direction - Maria Djurkovic - “Tinker, Tailor, Soldier, Spy”
Best Film Editing - Zachary Stuart-Pontier - “Martha Marcy May Marlene”
Best Adapted Screenplay - Hossein Amini - “Drive”
Best Visual Effects - “The Tree of Life”
Best Sound Editing - “We Need To Talk About Kevin”