The September 11 Commission’s 567-page final report has confirmed key facts presented in Fahrenheit 9/11.
These include:
Attorney General John Ashcroft told acting FBI director Thomas Pickard that he did not want to hear anything more about terrorist threats.  Confirmed, Commission Report at p. 265
After Bush was informed of the first plane hitting the World Trade Center, he went ahead with his classroom event.  After Bush was informed that the nation was under attack after the second plane hit, Bush stayed in the classroom for nearly seven more minutes, continuing to read with the children. Confirmed, Commission Report at pp. 35, 38-39.
Bush failed to have even one meeting to discuss the threat of terrorism with his head of counterterrorism Richard Clarke.  Confirmed, Commission Report at p. 201.
Bush failed to react to the August 6, 2001 security briefing, “Bin Laden Determined to Strike in U.S.” Confirmed, Commission Report at pp. 260-262.
142 Saudis, including 24 members of the bin Laden family, were allowed to leave the country after September 13. Confirmed, Commission Report at p. 556, n. 25  [Note that Fahrenheit 9/11 understates the number of Saudis who left.]
Individuals were interviewed by the FBI before being allowed to leave (although the report confirms that most individuals on these flights were not interviewed.)  Confirmed, Commission Report at p. 557, n. 28.
White House former counterterrorism chief Richard Clarke approved these flights. Confirmed, Commission Report at p. 329.

It should also be noted that the 9/11 Commission does not address or deem important a number of other issues either addressed in Fahrenheit 9/11 or revealed since completion of the film, including:

What exactly was the rush in getting these individuals out of the country so soon after the worst attack in U.S. history, why did Saudi Royals and bin Laden family members receive such special treatment at a time when most Americans still could not get flights (even though airspace may have been open), and how exactly were the flights arranged by the U.S. government?
Several unanswered questions posed by Senator Byron Dorgan (D-ND) in a July 20, 2004, Grand Forks Herald column: “At a time when 14 of the 19 terrorists from Sept. 11 were Saudi citizens, how and why were six secret flights allowed to sneak 142 Saudi citizens out of the United States in the days after Sept. 11 before they were properly interrogated? How do we know they weren’t properly questioned? Because Dale Watson, the No. 2 man and former head of counterterrorism at the FBI has said none of them were subjected to ‘serious’ interrogation or questions before being allowed to leave.  In fact, we now know that at least two and perhaps more of the Saudis who were allowed to leave after Sept. 11 were under investigation by the FBI for alleged terrorist connections.”
Information that came to light in Dana Milbank’s July 22, 2004 Washington Post article, including the fact that at least one bin Laden family member who was allowed to leave lived with a nephew of Osama bin Laden, who “was involved in forming the U.S. branch of the World Assembly of Muslim Youth” (WAMY), which the FBI has described as “a suspected terrorist organization,” and that the bin Ladens flew out of the country on the same airplane that “has been chartered frequently by the White House for the press corps traveling with President Bush.”
A full comparison of the findings of the 9/11 Commission and Fahrenheit 9/11 will be posted shortly.