The film also earned breakthrough performance honors for Isla Fisher and best on-screen team award for Vince Vaughn and Owen Wilson.
The unconventional awards show, held on a soundstage at Sony Studios, celebrates the fun of films with prizes recognizing the best on-screen hero, villain, kiss and fight, as well as sexy, funny and frightened performances.
Host Jessica Alba turned current blockbusters into comedic treats with parodies of "The Da Vinci Code," "Mission Impossible: III" and "King Kong."
"It was a lot of work" making the mini-movies, she said. "At the end of the day, I needed a bath and a cry."
Alba took home her own Golden Popcorn trophy for her sexy performance in "Sin City."
Jake Gyllenhaal was a double winner. He beat out Oscar-winner Reese Witherspoon for best performance and teamed with "Brokeback Mountain" co-star Heath Ledger for best kiss.
"This is a real honor, not just for me and Heath but for all of you, that you picked this movie and this kiss over all the other ones," Gyllenhaal said.
Awards are based on fan votes.
Rapper LL Cool J presented Spike Lee with the Silver Bucket of Excellence for "Do the Right Thing," his 1989 film examining racial tensions. The prize honors a movie from the past that has present-day resonance.
"The sad thing is that the issues that we tried to address with `Do the Right Thing' are still with us today, so how much progress have we made?" Lee asked as he accepted his award.
Will Ferrell presented fellow funnyman Jim Carrey with the MTV Generation Award for his diverse body of work.
"This man's versatility makes Thomas Jefferson look like a big fat idiot," Ferrell said.
Wearing an all-white suit, Carrey took the stage with a cadre of winged angels and performed a spontaneous hip-shaking jig.
The show also featured musical performances by soul duo Gnarls Barkley, rockers AFI and scantily clad songbird Christina Aguilera, who performed "Ain't No Other Man."
The show is scheduled to air at 8:30 p.m. June 8 on MTV.
A complete list of 2006 MTV Movie Awards winners:
Best movie: "Wedding Crashers"
Performance: Jake Gyllenhaal, "Brokeback Mountain."
Comedic performance: Steve Carell, "The 40-Year-Old Virgin."
On-screen team: Vince Vaughn and Owen Wilson, "Wedding Crashers."
Villain: Hayden Christensen, "Star Wars: Episode III-Revenge of the Sith."
Breakthrough performance: Isla Fisher, "Wedding Crashers."
Hero: Christian Bale, "Batman Begins."
Sexiest performance: Jessica Alba, "Sin City."
Fight: Angelina Jolie vs. Brad Pitt, "Mr. & Mrs. Smith."
Kiss: Jake Gyllenhaal and Heath Ledger, "Brokeback Mountain."
Frightened performance: Jennifer Carpenter, "The Exorcism of Emily Rose."
mtvU student filmmaker award: Joshua Caldwell, "A Beautiful Lie."
Silver Bucket of Excellence: Spike Lee, "Do the Right Thing."
MTV Generation Award: Jim Carrey.