These are NOT all one-ep links, so read them at your peril. They will often discuss multiple issues for different episodes.
Down the rabbit hole!
~ SPOILERS ~
There's a new tag, The Empty Fall and other S3 theory posts, which discusses these and more. Have some highlights...
The kidnapping in RF and a kidnapping footnote. Sherlock, you lying liar, aka a lookalike corpse?
Active errors, or continuity issue: blood on the pavement.
Another fail with The Plan, aka Team Awful Brothers/Deus ex Mycroft.
A really lovely piece about the waterfall aspect of Reichenbach combined with genius boredom.
No ordinary criminal... so it wasn't Mycroft after all! Bwahahah.
ETA: Box of hoaxes for Hearse, which I think I just fell in love with. Also the writer. Except, uh, I already adore Final Problem....