Jason Reitman's smash hit comedy also won trophies for Ellen Page (best female lead) and Diablo Cody (best first screenplay).
Director Reitman, however, was beaten to the directing Spirit Award by Julian Schnabel for The Diving Bell And The Butterfly which also won a cinematography award for Janusz Kamisnki.
The awards are presented to 'honour films made by filmmakers who embody independence and who dare to challenge the status quo.'
Other multiple winners included The Savages which won awards for best male lead (Philip Seymour Hoffman) and best screenplay (Tamara Jenkins) and I'm Not There which won best supporting female (Cate Blanchett) as well as the inaugural Robert Altman Award for ensemble cast.
Chiwetel Ejiofor won the best supporting male award for his part in Talk To Me, and Dan Klores won the best documentary for Crazy Love.
John Carney's Once from Ireland won the best foreign film, beating some of the year's most acclaimed foreign language films like 4 Months, 3 Weeks And 2 Days, The Band's Visit and Persepolis.
Scott Frank's The Lookout was named best first feature, while Chris Eska's August Evening won the John Cassavetes Award for best feature made for under $500,000.
Neil Kopp, producer of Paranoid Park and Old Joy, received the 11th annual Producers Award (an unrestricted grant of $25,000) which 'honours producers who. despite highly limited resources, demonstrate the creativity, tenacity and vision required to produce quality independent films.'
Ramin Bahrani, director of Chop Shop, won the Someone To Watch Award (also an unrestricted $25,000 grant) 'created to honour a talented film-maker of singular vision who has not yet received appropriate recognition.'
Laura Dunn, director of The Unforeseen, won the Truer Than Fiction Award (also an unrestricted $25,000 grant) presented to 'an emerging director of non-fiction features who has not yet received significant attention.'