Tyrion finds out which of three members of the small council (Pycelle, Varys or Littlefinger) is spying for his sister, by giving each suspect a different unique piece of information, and then seeing which one his sister finds out about. This method, commonly known as "Barium meal test" or "canary trap" (the latter term was coined by Tom Clancy in the novel "Patriot Games"), has been used in real intelligence agencies for decades.
The note that Theon writes to Robb, which is only briefly shown before he burns it, reads: "Robb, I hope this reaches you in time. My father has rejected the offer and plans to attack the North, raiding the shores and taking Deepwood Motte. Mobilize your army and make for the North before it's too late. I'll write again when I can. Theon". The scene was not in the book and was shot much later, as a transition before Theon's baptism. It was filmed on a minimal set, which is why the surroundings are completely dark.
In the novel, Renly's guard is called "Rainbow Guard". In the TV series it was changed to "King Renly's Kingsguard", due to the political connotations.
The episode title "What is dead may never die" is taken from a prayer used on the Iron Islands, by worshipers of the Drowned God.
Cersei tells Tyrion that the Martells loathe them. Indeed, the Martells (and the whole Dornish nation) hold a grudge against the Lannisters for the brutal murder of Elia Martell and her children by Gregor Clegane during the sack of King's Landing. Elia was married to Rhaegar, son of the Mad King, and when he was finally overthrown, the Lannisters reportedly ordered Clegane to wipe out every member of the Targaryen family.