Hi everyone!
Thought I'd chip in my thoughts on this... have tried to read the whole thread but haven't really had time so I do apologise if I plagiarise anybody's ideas!
OK so, my first question is, did Holmes know Moriarty was going to shoot himself? He certainly acted surprised and shocked when he did, and would no longer have needed to 'act' surprised at anything for Moriarty's benefit seeing as he was dead. If he didn't know M would kill himself, then he must have planned to fake his own death with the supposition that M would watch him fall from the roof... therefore would ideas such as him jumping into the rubbish truck and using a fake body really work? As in, surely M would see that happen and know it was fake?
Also, I can't help feeling that the dialogue scene on the roof just before M's suicide was strange. M is convinced that he has won and Sherlock is 'ordinary', and has just told Sherlock that he will never give the assassins the order to stand down. Sherlock then says something along the lines of 'I may be on the side of the angels, but don't think for one second I am one of them', then suddenly M is convinced that Sherlock has suddenly found a way to defeat him... but how? How does that line change M's mind and convince him that he needs to kill himself otherwise Sherlock will somehow force him to stop the assassins? Not sure if this is just me missing something obvious, or if it's actually significant.
Thirdly, I can't help feeling that IOU is definitely involved somewhere along the way... i'll be quite annoyed if it's just a red herring! It was graffitied on the wall outside of 221B when Watson runs back out for a taxi having discovered Mrs Hudson is not actually dying. What if when Holmes goes to see Molly to ask for her help, the 'you' he replies when she asks what he needs is not her as people have assumed, but the U bit of IOU? This is perhaps a little far-fetched :/
Finally, I think I remember reading somewhere on the thread that somebody suggested Holmes forgetting Molly's name earlier on in the episode and calling her 'John' is the significant clue that everybody missed that was out of character for him. Then somebody else suggested that actually this was just to show Molly's insignificance in Holmes' eyes (sorry for not having quotes for this, I can't find the posts again!). However, when Holmes goes to see Molly to ask for help he tells her she has always counted and he has always trusted her... therefore she isn't really insignificant so why would he have forgotten her name? Although if this is the clue I'm not sure what this would signify...
This has turned into a bit of a ramble rather than a proper theory, but just thought I'd share! What do people think?