In New York, the sound of bagpipes filled the 9/11 Memorial plaza in preparation for New York's 11th commemoration.
The ceremony consisted of the reading of the nearly 3,000 names of those who died in the terrorist attacks on the towers, musical interludes and moments of silence. Govs. Andrew Cuomo of New York and Chris Christie of New Jersey, and New York Mayor Michael Bloomberg were among the dignitaries attending, The New York Times said.
New York firefighter Gerard Chipura, whose firefighter brother, John, died on Sept. 11, told WNYC-TV, New York, he was worried people would stop commemorating the day after last year's 10th anniversary.
"It's heart-wrenching," Chipura said, "but you try to live every day the way your loved one would want you to live."
At 8:46 a.m., about the time American Airlines Flight 11 struck the North Tower of the World Trade Center in New York 11 years ago, a full Marine color guard emerged from the doors and flanked each side of an aisle that Obama and his wife walked as three bells tolled.
At the commemoration ceremony at the Pentagon, Obama said, "Even now, all these years later, it is easy for those of us who lived through that day to close our eyes and to find ourselves back there -- and back here -- back when grief crashed over us like an awful wave."
Eleven times the anniversary has been marked and Americans "have paused in remembrance, in reflection, in unity and in purpose," he said.
"But no matter how many years pass, no matter how many times we come together on this hallowed ground, know this -- that you will never be alone," Obama said.
Defense Secretary Leon Panetta said those who would attack the United States "unleashed our greatest strengths -- the spirit and will to fight back."
En route back to the White House, the president and first lady stopped at Arlington National Cemetery to visit the graves in Section 60, one of the sections where those killed in Afghanistan and Iraq are buried. They placed a "challenge coin" -- a medallion bearing insignia given out by commanders to motivate troops -- on one of the first graves they passed and spoke for several minutes.
Vice President Joe Biden traveled to Shanksville, Pa., where Flight 93 crashed after passengers and crew overwhelmed hijackers and brought the plane down.
Biden said it was "important that this memorial be preserved and go on for our children and our grandchildren, and our great-grandchildren, and our great-great-grandchildren -- because it is what makes it so exceptional."
"I also hope it continues to give you some solace knowing that this nation, all these people gathered here today, who are not family members, all your neighbors, that they've not forgotten," he said. "They've not forgotten the heroism of your husbands, wives, sons, daughters, mothers, fathers. And that what they did for this country is still etched in the minds of not only you, but millions of Americans, forever."
Republican presidential nominee Mitt Romney said "evil descended upon our country" 11 years ago.
"America will never forget those who perished. America will never stop caring for the loved ones they left behind," he said in a statement.
"On this most somber day, those who would attack us should know that we are united, one nation under God, in our determination to stop them and to stand tall for peace and freedom at home and across the world."
GOP vice presidential nominee Paul Ryan recalled seeing the smoke rising from the Pentagon 11 years ago.
"For me, this is a day to remember those who perished on that day of terror, including the first responders," Ryan said in a statement. "It is also a day to pay tribute to all those who have worked quietly and tirelessly both on the home front and abroad to prevent a repetition of such terrible events. And it is a day to give honor to those in our military who have sacrificed so much, including their lives, for the same end."
Congressional leaders planned to gather at the East Front steps at the Capitol, the same place members gathered on Sept. 11, 2001, to sing "God Bless America," Roll Call said.
At the U.S. naval air facility in Atsugi, Japan, a group of Japanese firefighters and American service personnel honored the victims of the attacks, Stars and Stripes said.
Firefighters, base emergency medical technicians and security personnel climbed 110 flights of stairs, the same number as in the New York City towers. Each firefighter wore a full uniform, complete with helmet and self-contained breathing apparatus, to create conditions similar to those New York Fire Department personnel would have experienced on Sept. 11, 2001, Stars and Stripes said.
Tom Kean and Lee Hamilton, former co-chairmen of the 9/11 Commission who now lead the Bipartisan Policy Center's Homeland Security Project, commended efforts at all levels of government to strengthen institutions that protect the country.
But, Kean and Hamilton said in a statement, several key areas of the commission's report still haven't been implemented, such as an interoperable, broadband network for first responders.
"As the years pass the danger exists that we will lose focus, divert attention to other concerns," they said. "But the threat of terrorism persists and our enemies continue to devise new ways to harm us. ... We owe it to the American people to keep our attention riveted on ensuring we are taking every step to keep the country secure."