In the opening shots we have Mycroft and Sherlock fighting over Sherlock tweeting...this is in marked contrast to the bond between them in TFP.
Sherlock refers to his 'big brother'.  In TFP, we meet his little sister.
Sherlock appears high, though he clams it's natural...foreshadowing of TLD.
Sherlock has a conversation with the seemingly insignificant Vivian, who comes to prominence later. Forum member Liberty has already highlighted the use of the seemingly insignificant women who actually play major roles. They are the great overlooked. As the possibility of a secret sister was overlooked by many.
Because of the doctored film footage, Sherlock is 'home and dry' apparently...but by TFP he is in deep waters.
Sherlock states that Moriarty filmed 'Miss me' before he died.  In TFP we learn he filmed lots of things.
Sherlock says Moriarty planned posthumous revenge and TFP shows how right he was.
Sherlock states he's the target...he certainly is for his sister.
All through this episode there are images of deep waters, usually behind Sherlock. Eurus specifically mentions deep waters in TFP.
Sherlock states 'it's never twins", when he and John are discussing cases...indeed, but we know it is a secret sister!
We see Sherlock connecting with Rosie, we see more of that in TFP.
We go from the image of the knackered parents to the girl on the bus. John checks his hair. We see John changing Rosie...this girl on the bus is going to become most significant.
Sherlock calls Greg 'Giles'. Says he's just kidding, then asks John his name(behind his back)- shows off he knows it's Greg and Greg is pleased!  By the end of TFP, Sherlock does know it's 'Greg'.
Sherlocck says "Most people are stupid".  He meets the cleverest in TFP.
Sherlock says 'daughter' when it's really a 'son'.  Was this Mark messing with us, over confusing a secret brother with a secret sister?!
(Again we  see a deep water image).
"Is your friend mad?" Charlie's Mum asks John.  Nope, we meet the mad one in TFP.
"I don't want to hit you" , Sherlock says to John about not sharing a taxi.  Little does he know John will give him  a kicking in TLD.
(We see shadows of deep waters again). Sherlock says he will wait for whatever's' coming...we know it's an East wind.
Mycroft said Sherlock never liked the 'appointment in Sumatra' story when he was a child. In fact he changed the character to a pirate.( reference to Redbeard).
Sherlock says he's having fun with cases while he can.  There is no fun in TFP...
Sherlock goes to the deep waters of the pool at the house.
We have the image of a clock moving on, this reminded me of Moriarty's ticking clock in TFP
Sherlock tells AJ that Mary is his friend and under his protection...doesn't work out well.
We are shown the memory of the Tibliski incident and Mary tells AJ "We die".  How right she was!
This episode centers on the importance of a code word...a bit like the importance of 'Redbeard'.
Mary says the team were like family. Sherlock retorts " Families fall out"...big time in the cases of the Holmes family.
Mary refers to " something from my past will come back to haunt me one day." The same is true for Sherlock.
Sherlock promises to keep Mary safe...only he doesn't.
Sherlock sees an image of 'Redbeard'. We see 2 children playing pirates.
Mycroft says it's hard to tell the difference between Sherlock and sentiment these days...this comes to fruition in TFP.
Mycroft warns that Mary may be retired in a permanent way...he's a prophet of doom.
"I need to do this my on way", Mary writes to John- and she does.
Sherlock says he's not familiar with the concept of happy families.  Thankfully we have the reunited family by the end of TFP.
John says to Mary "So many lies...and I don't just mean from you." More on this later...
"Mary I may not be a very good man". John says. Again we hear and see more of this later.
"I will keep you safe...in London".Sherlock promises Mary. "Come home and everything will be alright, I promise."..Heartbreaking.  
We see Mary's distress at the loss of AJ...nothing on John's distress later.
Sherlock makes the 'ammo' connection to 'I love you'- which of course is a code phrase in TFP.
We then get the full story of the girl on the bus...John sees her image in the plane window: this links to the Eurus child on the plane at the start of TFP. Girl signs herself 'E' and says 'This is me'.  We find out who 'E' is.
'E' actually texts 'Miss you' at one point...a clue?
We see a poster of Culverton Smith at the bus stop. This is a pointer to TLD.
At one point John is about to confess to Mary...he does in TLD.
Sherlock then heads for the 'deep waters' at the London Aquarium.
Vivian talks to Mary about wanting a family...we meet the whole Holmes family in TFP.
Sherlock deduces that jealousy was Vvian's motivation...in TFP we learn that Eurus was jealous of Sherlock having a best friend.
Mary takes a bullet for Sherlock...in TFP we see Sherlock prepared to shoot himself to save his brother and his friend.
Sherlock goes to comfort John. We see John's anger and we will see a lot more of that in TLD.
The deep waters images are behind both Sherlock and John...
John refuses to answer the phone to Sherlock.  In TFP he comments on Sherlock never answering his phone!
Sherlock goes to Ella to try and work out what to do about John.
We see Mycroft at home. He phones 'Sherrinford'.  We find out what this means in TFP.
(I only just noticed this time that the 'balloon John' is deflated, in the final shot of the flat. John is broken!)
Mary says she's giving John the hardest case of his career.
John wants anyone but Sherlock...that changes by TFP.
There is of course the keyword 'anyone' which features in TLD.
Mary asks Sherlock to save John...which he does in TLD and TFP.
Sherlock asks where does the road become a river?  Another 'deep water' reference and indeed we have the image of deep water behind him again.
Mary asks Sherlock to 'go to hell' to save John, which he does in TLD.