Okay, now that I've watched The Reichenbach Fall three or four times, I realize that there are some things that are bothering me...
1. Molly and Sherlock have the conversation about "you look at John like my dad did when he was dying when he thought no one was looking" in the lab at Bart's when they're analyzing the footprints. But this is way before Moriarty has revealed his endgame. So then why does Sherlock look like this? Is he just assuming that Moriarty's game involves him dying at some point? Is he already thinking he's going to have to fake his death? But he doesn't really seem to put that all together until they're outside Kitty's flat and he leaves John to go see Molly. Presumably he sets up his "suicide" with her then. So then what's going on with him in the lab? Is it about something else besides Moriarty?
2. Why is John upset about the media coverage? In Scandal he seems to be pleased that people are reading his blog and sending them cases. He even tells Sherlock "this is how you get your cases." So why, in Reichenbach, is he so nervous about it? Is it just because it's too much, too fast? He figures it can't last? Or is it something else?
3. In Baker Street, before the police come to arrest Sherlock, he accuses John of believing Donovan and thinking he's a fraud. Does he really think that? It seems authentic; this is one of the few times we've seen him lose his temper with John. Or is he sounding him out? He doesn't seem to have the same doubts when Moriarty "reveals" himself to be Richard Brook in Kitty's flat and Kitty is showing John the "evidence." Or is he just too shocked at Moriarty's game to react?
4. What's with the case Sherlock is working on just before Moriarty breaks into the Tower? He says, "Henry Fishguard didn't commit suicide; the Bow Street Runners got it wrong." It's an old case, because "Memoirs of a Bow Street Runner" is an old book. Also because John says "pressing case?" and Sherlock says "they're all pressing until they're solved." The Bow Street Runners were the first police force in London, started by Henry Fielding. But there's no hint of an actual, historical "Henry Fishguard" or (from what I can google) anything in the book about a faked or incorrect suicide. John did ask Sherlock to pick a small case (this is after the "be careful" conversation about the media coverage). And, of course, there's the mannequin. Is this a set-up for later? Is it a clue for John that he's going to fake his death? But this is quite early - Sherlock doesn't even know Moriarty is back at this point - why would he be thinking about faking his death? Is this the clue Moffatt's referring to that everyone is missing?
5. Who arranges the call to John with the "news" about Mrs. Hudson? Is it Sherlock? Or does he just deduce that Moriarty will do it? He's obviously not surprised and he obviously knows Mrs. Hudson's not really in danger (and, after all they've been through, how can John believe that he would react like that? Argh, John!). But if it is him, he must know that John will come back as soon as he sees that Mrs. Hudson is okay. Why wouldn't he do something to send John away for a longer period of time, until he's done with Moriarty? Presumably he doesn't know about the hit men at this point. Does he think he'll have Moriarty sorted by the time John gets back? Does he think that John will be gone if he has to fake his death?
6. How much of Moriarty's game does Sherlock have figured out on the roof? He sounds surprised about Moriarty's plan to have him jump, but of course he's not, since he's already put his own measures into place. Does he know the key isn't real? Does he know about the hit men? Does he think Moriarty is insane enough to kill himself? What's real surprise and what's him playing Moriarty?
7. Does no one on the police force think of looking for Sherlock at Bart's? He is a fugitive. Wouldn't that be the first place they'd look (after Baker Street)?