Allright, here’s some of my favorites. Heed the warnings cause some of these are dark. Also I started reading Torchwood fic before I dicsovered AO3, so these are elsewhere. Chance’s Archive is where I started:
Supertemp (this ones on LJ, so you have to go one chapter to the next)
Jack Harkness – Super Temp 1
Summary: Jack Harkness works in a cubicled office as a temp and leads a boring, gray life. Then one day he meets a blue eyed man and things begin to change.
Warnings: Violence, domestic abuse, sexual abuse, rape, angst, h/c, torture
There’s a couple others in that universe and dealing with the aftermath
The Lighthouse and the Dark – Miss Winterhill
Jack hates the dark. Ianto hates it when Jack dies. Jack gets injured on a mission and they have to confront their fears.
Warnings: Explicit sex, self-harm, power games and mild bdsm (and temporary death of the Jack Harkness type)
Theosis – Ceefax
AU. Jack visits a monastery in search of information, and finds a whole lot more besides.
There’s smut in this one too, but it’s also very sweet.
That might get you started. I’ll be happy to toss more your way. There’s a pwp fic involving an ice lolly if you want something fluffy. and some other kinky pwp fics I could recommend.
Also there is a COE fix it fic I’ve never been able to find again, I know it was on lj, but yeah, I’ve never found it