I'm posting this in the S3 section as the post to which I'll link further down the page has big honking spoilers for both episodes 1&2 of S3.
Basically, this is a meta discussing John Watson's sexuality, his perception of it with regards to himself and society and how that differs from his perception and acceptance of others. It is well worth a read and quite thought provoking and addresses John's constant protestations of "I'm not gay!" in a way you might not have considered. It also touches on Mary and John's relationship both to each other, and with Sherlock.
So, go read... The Case of John Watson's Sexuality on livejournal.