I will try to stay away from what Christian has already posted which already is a great answer. I can answer this from a reader's perspective.
Sherlock holmes stories by Doyle can be classified into Long stories and short stories. There are only 4 long stories of which 2 of them are already made into episodes two of them which haven't made it into episodes are the Sign of Four (If rumors are true I think there is a sign of three planned for Season 3 I think thats that adaptation) and Valley of Death (Although I hardly doubt we will see an adaptation of that because this story has a link to Moriarity since he is dead in the series we can put this out of the question). As for the short stories there are 56 short stories which are classified into Adventures, Memoirs, Return and the His Final Bow categories.
The stories the episodes are based off mainly are as follows.
A Study in Pink - A Study in Scarlet (Long story)
The Blind Banker - Mostly based off Five Orange Pips (Short Story)
The Great Game - Mostly based off The Adventure of Bruce Partington Plans (Short Story)
A Scandal in Belgravia - A Scandal in Bohemia (First short story in Adventures of Sherlock Holmes)
Hound of the Baskerville - The Hound of the Baskervilles (Long Story)
The Reichenbach Fall - Final Problem (Last short story of Memoirs of Sherlock Holmes)
To closely relate to the attention to detail given by the creators of the show In the first episode Study in pink when anderson sees the pink lady's body with word Rache written on the floor he surmises that Rache could be a german term referring to Revenge actually but sherlock dismisses him saying that it was indeed intended to be Rachel but in the book its actually the other way, The police start to look for a girl named Rachel and then Sherlock holmes asks them to stop looking for Rachel and says that Rache means German for Revenge.
In the great game too. The plot's core was straight off the short story, in the book it was plans for submarine but in the episode it was a missile program which gets stolen, The same character name Andrew West who dies and the part where the body gets placed near a train tunnel all were right of the short story.
The Hound of the Baskerville was significantly changed from a family plot motive in the book to a biological weapon in the series mainly because creators didn't want to show a hound in the episode they wanted it to be modern so current viewers can relate but the core of the story is driven by the characters created by Doyle.
There were also even other stories referenced in the episodes like the Story of the Geek interpreter (Adventure of the Greek Interpreter), Speckled Blonde (Adventure of the Speckled Band etc). The best part about the show is that it's got equal amount of content for readers and non-readers alike to enjoy about the show. it's not like ones who haven't read the stories won't enjoy the show at all.
These are the specific references I could think of right now. I will update this answer if something else comes to my mind.