The Journal, the only multiple winner this year, also won in international reporting for its coverage of how capitalism is emerging in China.
Kenneth R. Weiss, Usha Lee McFarling and Rick Loomis of the Los Angeles Times won for explanatory reporting for their "Altered Oceans" series about how sea life is being killed by trash and other human impacts.
The judges also praised their print and online stories.
In awarding the public service prize to the Journal, the judges cited its "creative and comprehensive probe into backdated stock options of business executives that triggered investigations, the ouster of top officials and widespread change in corporate America."
The staff of The (Portland) Oregonian won for breaking news for its reporting on a California family that disappeared in the mountains during a blizzard. James Kim and his family took a wrong turn while returning home to San Francisco following a Thanksgiving trip. Kim was found dead of exposure after his wife and two young daughters were rescued. The judges praised the newspaper for its "skillful and tenacious coverage ... telling the tragic story both in print and online."
"Our thoughts today are with the Kim family, for, as our reporting showed, this is a tragic accident that might have been avoided," Executive Editor Peter Bhatia said.
Brett Blackledge of The Birmingham (Alabama) News won for investigative reporting for his exposure of cronyism and corruption in the state's two-year college system. The stories resulted in the dismissal of the chancellor and other corrective action, the Pulitzer Board noted.
Charlie Savage of The Boston Globe won for national reporting for his revelations that President Bush often used "signing statements" to assert his controversial right to bypass provisions of new laws.
"This is a great honor, and I view it as a great moment not just for myself but for the Globe as an institution," Savage told The Associated Press. "The Globe for a while was throwing it out on the front page when a lot of people were ignoring it, and that took a lot of courage."
Debbie Cenziper of The Miami Herald was honored for local reporting for reports on waste, favoritism and lack of oversight at the Miami housing agency.
Andrea Elliott of The New York Times won for feature writing for coverage of an immigrant imam striving to serve his faithful in America.
The Daily News of New York was honored for editorial writing for its editorials on behalf of Ground Zero workers.
Cynthia Tucker of The Atlanta Journal-Constitution won the commentary prize.
Newsday's Walt Handelsman was honored for editorial cartooning.
Jonathan Gold of LA Weekly was cited for criticism for his restaurant reviews.
The AP's Oded Balilty won for breaking news photography for his image of a lone Jewish woman defying Israeli security forces as they remove illegal settlers in the West Bank.
"It is a stunning single image that captures the chaos and emotion of that evacuation," AP Executive Editor Kathleen Carroll said in a message to the staff.
Renee C. Byer of The Sacramento (Calif.) Bee was honored for feature photography for her portrayal of a single mother and her young son as he loses his battle with cancer.
In addition, the Pulitzer board gave special recognition to Iranian photographer Jahangir Razmi, whose 1979 picture of a firing squad in his native country won the 1980 Pulitzer for spot news photography. He remained anonymous until a Wall Street Journal reporter unmasked his identity in a December article.
In arts categories, the prize for general nonfiction was awarded to Lawrence Wright for his book, "The Looming Tower: Al-Qaeda and the Road to 9/11," a penetrating analysis of how Islamic fundamentalism has reshaped the world.
Cormac McCarthy won for fiction for his sparse, apocalyptic novel, "The Road."
Debby Applegate won for biography for "The Most Famous Man in America: The Biography of Henry Ward Beecher," the 19th century abolitionist and preacher.
"It took me about 20 years to write this book from the time I stumbled upon Beecher's work and thought I'd write a college seminar paper on him," said Applegate, 39, who studied at Amherst College as an undergraduate.
David Lindsay-Abaire won the drama prize for "Rabbit Hole," about a wealthy, suburban couple trying to come to terms with the death of their young son, Danny, accidentally killed when he runs into the street and is struck by a car. The jury had deadlocked on three entries in the drama category.
Jazz artist Ornette Coleman won the music category for "Sound Grammar," his first release in a decade and only the second Pulitzer won by a jazz composer. Wynton Marsalis won the music prize in 1997 for "Blood on the Fields."
Coleman said his cousin notified him that he had won the honor. "I didn't believe him," Coleman told The Associated Press. "I'm grateful to know that America is really a fantastic country."
Natasha Trethewey, a professor of creative writing at Emory University, won for poetry for "Native Guard," a collection that honors the black soldiers who played a role in protecting a fort on the Mississippi coast during the Civil War. The racial legacy of the war echoes through the poems and a forgotten history of the South, according to publisher Houghton Mifflin.
Special citations were given to science fiction icon Ray Bradbury, 87, and famed jazz saxophonist John Coltrane, who died in 1967 at age 40.
Winners in every category except for public service receive a $10,000 cash award and a certificate. The public service winner is awarded a gold medal.
The awards are given by Columbia University on the recommendation of the 18-member Pulitzer board.
The board this year replaced the beat reporting category with a local reporting category.
Online material was allowed to be part of all entries for the first time last year, but was restricted in all but one category to written stories or still images. This year, newspapers were able to submit online material like video, blogs, databases and interactive graphics for all print categories. The Public Service category has allowed material such as streaming video and databases since 1999.
The Pulitzers were created under the terms of the will of newspaper publisher Joseph Pulitzer, who died in 1911. He endowed the journalism school at Columbia, and dictated that money be set aside for the prizes. The first awards were handed out in 1917.
On the Web: www.pulitzer.org