The following are the endings for the PC/Xbox 360 version.
Best - If Sam stops the destruction of the cruise ship, saves the CIA Agent Hisham, and saves Lambert / shoots Jamie Washington, or only two of these with NSA trust above 33%, then Sam evades capture by the SWAT team (who, along with the rest of America's agencies are unaware of Fisher's NOC status) and escapes the compound, incapacitating a SWAT member and donning his stolen kit. The NYPD pursues Fisher through New York, but he evades capture and jumps into the river, where he swims to a stolen US Coast Guard vessel commandeered by Carson Moss along with Massoud ibn-Yussif's Red Mercury bomb. Fisher kills Carson, disarms the bomb and escapes the boat seconds before it is destroyed. This ending is seen as the most canonical as it is the only ending which concludes with a 'To be continued...'
Normal - If Sam kills/destroys two of the three targets or saves all three with NSA trust below 33%, Sam is captured by the SWAT team. He is charged with murder, and conspiracy to commit terrorism. To this, he pleads 'not guilty'. Before his trial begins, however, Sam breaks out of prison and is on the run.
Worst - If Sam kills/destroys all three targets (alternatively, kills/destroys two targets but trust with the NSA is below 33%), he is initially captured by the SWAT team, however, utilising a smoke grenade during his arrest, he escapes.