He said that on his first day in office he would give commanders there a new mission - to end the war.
On the Guantanamo cases, military judges have agreed to suspend six trials. They include proceedings against five men accused of plotting the 11 September attacks.
The judge halted their trial despite the fact that four of the five - including alleged 9/11 mastermind Khalid Sheikh Mohammed - opposed the proposed suspension during a court hearing on Wednesday.
Earlier, the judge in the separate trial of Omar Khadr - a Canadian man accused of killing an American soldier in Afghanistan in 2002 - also agreed to suspend the case.
Meanwhile the US Senate, which traditionally moves swiftly to approve a new president's Cabinet, has confirmed the appointment of Hillary Clinton as secretary of state. She was endorsed by a 94-2 majority on Wednesday.
The vote had been postponed after a Republican senator demanded a debate about foreign donations to a foundation headed by her husband, former President Bill Clinton.
On Tuesday the Senate approved six Cabinet members, including Janet Napolitano as homeland security secretary and Steven Chu as energy secretary.
Several other positions are still to be confirmed.
Timothy Geithner, the nominee to head the treasury department, faced the Senate finance committee on Wednesday to explain his initial failure to pay payroll taxes he owed while working for the International Monetary Fund.
He apologised to the committee, saying he had been careless but that he had "paid what I owed".
Mr Obama last week called Mr Geithner's tax problems an embarrassment but an "innocent mistake".
Other Obama nominees still to be confirmed are Eric Holder as attorney general, and Tom Daschle as head of health and human services.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.