I'd love to nominate The Curious Case of the Boy in the Raincoat, which is both Irene/Sherlock and John/Mary mystery/adventure with a side of Nero Wolfe, and a lot of John POV (perhaps better to say his descent into disbelieving madness) and a lot of exploring John and Sherlock's friendship.

Unfortunately, being the beta for the fic means I'm pretty certain it'd be a little conflict-of-interest-y if I ran a discussion on it. So I'd really love to solicit someone who isn't conflicted to run a discussion on it!