I'm pretty sure the clue was right in front of us during TRF. John went to Mycroft's office at dawn on the day of the suicide hoax and criticised him for giving info about Sherlock to Moriarty. But I've been certain for months that Mycroft was the organizer of the suicide hoax, and the thing which Sherlock did that was "out of character" was asking Mycroft for help in executing the planned hoax.
I think Sherlock first realized he needed to fake his suicide just 12 hours before he actually jumped -- when he was in the street outside Kitty's house late at night, walking back and forth and talking rapidly. He said, " . . . there's only one thing he needs to complete his plan, and that's to -- "
He stops and then says to John, "There's something I have to do."
I think Sherlock came up with the initial plan right there -- not days or weeks in advance. And immediately after that, he spoke with Molly and then called Mycroft to start the process of organizing the suicide hoax.
So, the clue which everybody missed was the fact that Holmes was willing to ask for help in executing his planned suicide. His extreme change in attitude made the plan possible, with the help of Mycroft, Molly, and all the people they employed to conduct the operation.
I know I'm not the only one to present this idea, but there are many people who seem to be looking for tiny details they can turn into dramatic revelations, and I don't think these theories are the answer to the quesiton.