More of a suspicion than a theory at this point, but let's see what you think...
Okay, so Moffat
told a Radio Times reporter that there's a big old clue in Reichenbach that we're all missing. Specifically "something Sherlock did that was very out of character".
Now, assuming that he wasn't jerking our collective chain here (which is one hell of a big assumption), my guess for that very OOC thing is:
Singing.
Seriously, was I supposed to get scared when he did that? Yikes.
Anyway. I noticed there was a lot of Bach in this episode (Reichen-Bach, get it? Har har): Sherlock is playing a Bach piece as Moriarty creeps up the stairs to meet him ("Johann Sebastian would be appalled"), and Moriarty claims that his "binary code" finger-tapping was simply him drumming his fingers to a Bach tune ("Partita Number 1; thank you Johann Sebatian!").
Despite his rantings to the contrary, I reckon Moriarty really does use some sort of secret "key" in this episode: a musical key. A musical key relating to Bach; most likely a series of notes (his mp3 player WAS going full blast during each of the break-ins). And I think Sherlock singing the "I don't have to die if I've got you" line is his way of letting dear old Jimbo know that he's onto him.
Digging a little deeper, some Google-fu turns up the interesting fact that Johann Sebastian Bach apparently used Gematria numerology in his music. In plain English: he assigned certain letters of the alphabet - and certain musical notes - a numeric value, and used this simple number code to implant secret messages in his compositions.
So, each note of a musical passage = a certain number, and the whole passage = a whole line of numeric code?
What if the "I've got you" notes Sherlock sings at Moriarty are Moriarty's own secret number code to call off the snipers?
Then there's Jim's not-very-subtle repetition of the letters "I.O.U." It's possible that the letters IOU translate into a number code in Bach's Gematriac system...but interestingly, if the letters IOU are taken out of a police lineup of vowels, that only leaves A and E. Which, aside from the part of a hospital you never want to find yourself in, are also musical "keys".
Either way, I reckon we'll see an explanation very along those lines in s3. Why? Because Moffat is a massive Doctor Who geek, and because I have seen The Five Doctors:
Remember that bit where the "key" to get into Borusa's secret lair was a piece of music? (Hey, our Moffat only steals from the best.) :)
Whaddaya think, sirs?
Q