He says, 'Rose Tyler, I love you too'.
You don't hear it, of course, but it's obvious from context—and confirmed by the producers.
She's just asked the two Doctors what they were unable to say the last time. She's referring to the end of "Doomsday", when she tells the Doctor that she loves him, and he starts to answer, 'Rose Tyler', but then fades out of her universe before he can finish. When we see him back in the TARDIS, he's saying 'I…', and crying.
So, when Rose asks what he was unable to say last time, the 'main' Doctor doesn't answer, but the Meta-Crisis Doctor whispers what he'd tried to say that last time, and she kisses him. So it can only be 'Rose Tyler, I love you too'.
In Confidential, Russell T Davies (writer and executive producer) says that of course the Meta-Crisis Doctor told her that he loves her, and Julie Gardner (his co-exec) later brings it up again and says the same thing.