*much spoiler alert*
On the subject of the canaries - it's a throwaway reference in the opening paragraphs of the story "the adventure of Black Peter"
- "In this memorable year '95 a curious and incongruous succession of cases had engaged his attention, ranging from his famous investigation of the sudden death of Cardinal Tosca—an inquiry which was carried out by him at the express desire of His Holiness the Pope—down to his arrest of Wilson, the notorious canary-trainer, which removed a plague-spot from the East-End of London."
It's never referred to again (i don't think) by ACD, but seems to have been picked up by a number of others when writing pastiches and new adventures.
Also - J.P., thanks for posting the "Reigate Squires" reference - one of my favourites from the new series.
I'll add one which we've not discussed yet, if I may. In ACD's originals, of course, Watson's first wife Mary dies - though this time during the 'great hiatus' between 'the Final Problem' and 'the Empty House.' In Doyle's stories, she dies of TB, which commonly manifested as a lung problem - while in the series, she dies of quite a different chest complaint!
I also thought that A.J. from the "A.G.R.A" group could be Henry Wood from "the Adventure of the Crooked Man" - another character who was tortured dreadfully after a betrayal, and returned to England after many years.
A.G.R.A, of course, comes from "the sign of the four" - the second Conan Doyle novella, in which Mary Morstan is introduced to John Watson, and they are later to marry. In the story, she is the unwitting heir to one-fourth of the 'Great Agra Treasure.' In the story, Watson feels he can only honourably ask her to marry him once it is confirmed that the treasure is lost. Likewise in the series, it's only after the loss of the A.G.R.A memory stick (one-fourth of the 'great agra treasure') that their relationship can continue.
The list goes on, and on, and on. I particularly liked when Craig, Sherlock's hacker friend, refers to Thatcher as being 'like Napoleon' - it's been noted already that 'the six Thatchers,' and the storyline of the busts, and the 'black pearl of the Borgias' all come from 'the Six Napoleons.
I'm a huge fan of Doyle's stories, and have spent a lot of time on different adaptions, too, but I can't help but feel that 'Sherlock' is one of the most lovingly adapted versions of Doyle's originals that I have ever seen.
Wonderful stuff, and glad to have a place to discuss these things now, too.
P.