Other best-picture nominees were "American Gun," a drama about the proliferation of firearms in America; "The Dead Girl," a thriller centered on a serial killer's female victims; and "Pan's Labyrinth," a Spanish-language tale about a girl's dark fantasy life in Fascist Spain.
Maverick filmmaker Robert Altman, who died last week, earned a best-director nomination for his final film, "A Prairie Home Companion." The new James Bond, Daniel Craig, received a supporting-male actor nomination for the Truman Capote drama "Infamous," in which he plays a death-row inmate.
The Spirit Awards, formerly known as the Independent Spirit Awards, honor films produced on comparatively small budgets of less than $20 million. The awards will be presented Feb. 24, the day before the Academy Awards.
"Little Miss Sunshine," the summer mini-hit about a dysfunctional family's comic trek to a child's beauty pageant, also earned two supporting-actor nominations, for Alan Arkin and Paul Dano. Stars Greg Kinnear, Toni Collette and Steve Carell were shut out in the lead-acting categories.
The film also was nominated for best director (husband and wife Jonathan Dayton and Valerie Faris) and best first screenplay (Michael Arndt).
"Half Nelson" earned lead-acting nominations for Ryan Gosling, who plays an inspiring inner-city teacher with a drug problem, and Shareeka Epps, who plays a promising student who becomes both his pupil and counselor.
Ryan Fleck earned two nominations for "Half Nelson," for best director and first screenplay, co-written with Anna Boden.
Other nominees for best female lead were Catherine O'Hara, "For Your Consideration"; Elizabeth Reaser, "Sweet Land"; Michelle Williams, "Land of Plenty"; and Robin Wright Penn, "Sorry, Haters."
Joining Gosling in the best male lead category were Aaron Eckhart, "Thank You for Smoking"; Edward Norton, "The Painted Veil"; Ahmad Razvi, "Man Push Cart"; and Forest Whitaker, "American Gun."
Supporting-actress nominees: Melonie Diaz, "A Guide to Recognizing Your Saints"; Marcia Gay Harden, "American Gun"; Mary Beth Hurt, "The Dead Girl"; Frances McDormand, "Friends with Money"; and Amber Tamblyn, "Stephanie Daley."
Along with Arkin, Craig and Dano, supporting-actor nominees were Raymond J. Barry, "Steel City," and Channing Tatum, "A Guide to Recognizing Your Saints."
The Spirit Award nominations mark the beginning of a flurry of key awards announcements leading up to Jan. 23's Oscar nominations. December brings Golden Globe nominations, best-of-the-year picks from major critics groups and other film honors.
Photos: Scenes from "Little Miss Sunshine"
Photos: Little Miss Sunshine New York Premiere
Photos: The Life of Robert Altman (1925-2006)
Since they honor independent and sometimes obscure films, the Spirit Awards often do not reflect the overall field that will compete for the Oscars and other high-profile Hollywood awards. Last year, though, many key Spirit and Oscar nominees overlapped, including "Capote," "Brokeback Mountain" and "Good Night, and Good Luck."
Nominees were chosen by members of the nonprofit cinema groups Film Independent and the Independent Film Project.
By David Germain