One thing that's been bugging me is the sniper who was trained on John his scope followed John all the way through to after Holmes' Body was carried off. that meant that his vantage point had an unobstructed view of the point of impact. ergo! he (of all people) would have seen the way Sherlock faked it and as he lived t put down the rifle we have to assume that for some reason he elected to not act on the knowledge that Sherlock didn't meet his end of the bargain.

here a theory i have
He was bought off. It's possible that while Moriarty was in custody, Sherlock and Mycroft had also already "pinched" Moriarty's preferred triggermen and made them counter-offers. Not just monetary but as Mycroft was in the government he could ensure the triggerman/men that they would be given full immunity/pardons and yes rewards for simply playing at being on Jim's side.

I'm not sure if this has been mentioned already but when in SiB Sherlock and John are walking through a theater:
SH: So what're you going to call this one? "The Belly-Button Murders"?
JW: Uhm....."The Navel Treatment"? (After "The Naval Treaty)

A Good luck kitty (Blind Banker)
A Skull (Study in Pink)
Everything's burning (the Great Game) 

Yeah I'd say that Tattoo definitely is appropo! 
Well done sir! (particularly if you got that just for it's own merits and realized the underlying connections after the fact!
 

Before Sherlock came back probably but after his return was announced I'm sure Lestrade might have dropped by (off-camera) and told John some of it. (plus there were some cutaways in the reunion including them going tfrom one resturaunt to another so Sherlock himself might have already been aware of The Empty Hearse)

I started thinking about the Anderson scene and the thing that came through to me was that the camera is on John in the Tube Car it flashes White we get the Sherlock explains scene then it flashes white again and we're back in the Tube Car where Sherlock starts laughing. that to me says the entire sequence is how John is imagining what Sherlock would say if he wanted to explain it. and Anderson is John's mind saying there's no way that of all the people Sherlock would tell the last person to hear the truth would be Anderson (he'd have to get it through the grapevine not from the horse's mouth!)

Finished Collecting all of the Jeremy Brett series 
Collected all of the Basil Rathbone Series
Watched Elementary (It's not a bad show IMHO)
bought Sherlock the casebook
Watched the Robert Downey Jr. Films 
Watched Star Trek Into Darkness
Re-watched (ad-nauseum) the first six SHERLOCK Episodes as well as the Pilot version of a Study in Pink as well as all associated special features
Watched the Sherlock facebook page daily for news about series three
Shared any videos of clips and/or trailers pertaining to Series 3
Created this banner for my facebook cover

and this for my profile picture

Suggested Benedict take over the reigns as another British Hero using this as the basis:

Read several of the original Canon
Bought the Complete Sherlock Holmes Encyclopedia by Jack Tracy
watched Series 3 of Sherlock on Youtube as soon as it was available before the first Episode even airs on PBS
Downloaded the ringtone edit of staying alive , put it into my parents itunes libraries uploaded it into their phones replaced my ringtone name and picture with Moriarty's
rang them up Christmas Morning (Amused the hell out of them and made my older sister facepalm)
I'm sure I did more but those were the clearest in my mind as of this writing