Good thing you commented, or I would have forgot :x

Okay, I trawled my memories - here's some more -

http://wallhaditcoming.livejournal.com/866.html
Caring is a Mistake - Don't be fooled - it only starts out fluffy...

http://verityburns.livejournal.com/5447.html
The Heart in the Whole - This is a loooong one, and just brimming with John angst.

http://ladyflowdi.livejournal.com/641930.html
Infiltrate - another long one, very plotty. Seriously amazing fic.

http://s0mmerspr0ssen.livejournal.com/3399.html
The Punishment - Mycroft is under the impression that John hurt Sherlock in some way, and punishes him. Non-con.

http://loveslashangst.livejournal.com/68046.html
Medic - John and his nightmares.

http://etothepii.livejournal.com/5347.html
They Tell Me Their Secrets - more telepathic!John.

http://10leaguesbeyond.livejournal.com/39138.html
Apotheosis - a reversal of the Empty House scenario, where John is presumed dead and goes after Moriarty.

http://amavissem.livejournal.com/13022.html
White Lies Like Cyanide - John drinks poison meant for Sherlock.

http://thenorthwing.livejournal.com/6293.html
Sound of Solitude - John believes that Sherlock is dead.

http://velvet-mace.livejournal.com/330979.html
Droit de Seigneur - in which Mycroft is an evil overlord, and John is a BAMF.

http://velvet-mace.livejournal.com/330064.html
The Spirit Child - seriously fucked up and nightmarish one-shot.


And here's a link to a Sunday Recday post on sherlockbbc - the theme for that week was Watson-centric fics.
http://sherlockbbc.livejournal.com/2484837.html

Good god, look at all that. I feel like I should call up Martin Freeman and apologize...