Director Sofia Coppola maintains that Bill Murray's final line to Scarlett Johansson in Lost in Translation (2003) was unscripted and that no one, including her, knows what Bill Murray said except for Murray and Scarlett Johansson.  During the scriptwriting process, Sofia wrote several different lines for the end of the film, but didn't like anything she wrote.  The final draft of the script says Bob tries to tell Charlotte he loves her but he can't muster the words.  It was planned that Bill Murray would improvise the ending line as he wished.  Incidentally, the final kiss was also an improvisation.

The often-asked question finally has been answered by the creator of the video below.  Bob whispers into Charlotte's ear, "I have to be leaving, but I won't let that come between us. Okay?"