Here's a bunch of fic recommendations for excellent Torchwood fics that I've had bookmarked. Many of these are from the old days of Torchwood fandom and never got transferred to ao3, so there are quite a few livejournal links and a few wayback machine links. Anything that I had bookmarked on lj that got transferred to ao3, I'll link the ao3. I may put my own notes/descriptions in brackets after the fic summary.
Proof Of Your Existence by sarcasticchick - Can you offer me proof of your existence? How can you? When neither modern science nor philosophy can explain what life is. [In which Ianto is more than what he seems.]
What Lies Within by xtricks - Ianto becomes contaminated with an alien. Jack will do whatever he can to hold onto him, even as he changes. [Link goes to the last chapter, which has all the others linked. TW: tentacle sex, which is partly metaphorical and partly literal.]
Conversational Japanese, Plus Frogs by james - Tosh and Ianto have been taken prisoner. They cope.
PTSD: Post Torchwood Stress Disorder by waldo - It's been two and a half years since Canary Wharf. It's been a year since Lisa. And Jack is just now realizing what the real toll has all been on Ianto and the other survivors of Torchwood One. Now he needs to fix a big thing done badly before anyone else dies.
Notebird by cyus - A note points to nowhere and a bird comes from nowhere, and Torchwood, in the wake of their teammates’ deaths, finds that some experiences shatter things into pieces too small to be fit back together.
Second Look by remindmeofthe- Sometimes, you get a chance to see the past through a different pair of eyes: your own.
The Cartography Of Feeling by sholio - "We're sodding gladiators," Owen said. "Fuck this entire day and Jack Harkness too." (Or: Owen and Ianto are abducted by aliens and forced to arena-fight. But the worst part might be the control device that connects them in an emotion and pain-sharing bond.)
Forget, Survive, Repeat by d8rkmessngr - He came to Torchwood, to Jack, for Lisa. But now she's gone and Ianto isn't sure what there is he has left. Post "Cyberwoman".
I Had No Idea I Had Been Travelling by kalichan & rm - It's not how you die; it's how you live, especially when your life is built of stories. And in the end, all lives are. [This fic is incredibly long, but it is absolutely beautiful, and most of the segments can be read individually. I'm of the opinion that everyone should read this fic. It's the Torchwood fic I continued to think about for years even when I was focusing on other fandoms.]
Hourglass by lazuli - Death is not the only form of loss. Torchwood grieves the loss of Owen and Tosh, and something strange is wrong with Jack. [Link goes to wayback machine, but all chapter links work.]
The Cricket And The Bird by solsticezero - On the nature of immortality and the longevity of birds.
Like The Wind by clarrisani- Sometimes all you can do is run. [Mild Owen/Ianto, leaning closer to friendship.]
More Richer Than My Tongue by sanginmychains - Ianto needs to get some space after the events of Cyberwoman. Jack comes along. They get rained on, and discuss their relationship.
Got That Friday Feeling Again by NancyBrown - HELP HELP HELP HELP I AM TRAPPED IN A TIME BUBBLE The magic marker all over the nice chintz wallpaper bled and smeared as Owen wrote in increasingly desperate lettering across the walls. Ls and Ps dragged down, wiggly at the end or drawn out in slashed strokes.
I Am Not My Own by methylethyl - "Torchwood's disability pay is about this big--" Ianto held up his thumb and index finger, about two centimeters apart. "--and comes out of a gun at a thousand meters per second."
Disinterred by seize - "What is a man? A miserable little pile of secrets." Ianto makes a discovery, and learns there are things he probably doesn't want to know. He asks anyway. [TW: torture.]
Frames Of Reference by echo - There's a difference between 'mostly alive' and 'mostly dead'. Sometime it's just hard to remember which one is which, especially when you get right down to the details.
Do Not Go Gentle by mcparrot - Reeling from the deaths of Owen and Tosh, Gwen and Ianto watch helplessly as Jack acts erratically. They assume it's just his way of mourning - until he disappears.
Tea And Sympathy by osprey_archer - Soon after Jack's disappearance, Owen takes sick. Ianto goes to check on him. [Some wonderfully unhinged Owen/Ianto fic]
Before You Know It by yuma - In all honesty, he should have been expecting it. He was there when boys, not yet men, suffered what was first called shell-shock, then combat fatigue, to the neatly packaged politically correct acronym.
Sweet, Delicious Despair by marchling - A group of strange suicides comes Torchwood's way when the police can't figure out why happy people with everything to live for are suddenly taking their own lives for seemingly no reason. The team is on the case, but there are no leads… Until one of their own is threatened. [TW: Suicide]
The Subject Of Mourning by jesuisgourde - Gwen had said Those poor girls. But both were dead, victims of Torchwood, of circumstance, of the most destructive kind of loyalty and love. Owen could only think Poor Ianto. The dead were dead. The living had to keep living with the pain. Owen and Ianto in the immediate aftermath of Cyberwoman.
In Your Image by blackbird_song - Jack and Ianto sitting in a tree: Torchwood-style.
Object Permanence by solsticezero - After the events of Exit Wounds, Ianto is left with lingering anxieties about the safety of the people he loves.
[a brief interlude for paperclipbitch fics. she's been my favourite torchwood writer since the early days. please read all of her stuff.]
If You Pass Go, Do Not Collect £200 by paperclipbitch - Ianto is sent to rescue Owen from 19th Century London, but he’s less than impressed by what Owen has been doing to survive.
Untitled Series 2 AU by paperclipbitch - “Come on,” Ianto sighs, and Owen falls into his side like he's just been waiting for the invitation. [Owen/Ianto]
Clinging To The Wreckage Until I Got The Message by paperclipbitch - “You need something other than this in your life, Owen,” Ianto murmurs. [Owen/Ianto]
People That I Wasn't by paperclipbitch - Jack and Ianto have to deal with death in all sorts of ways.
Hamartia by paperclipbitch - “Don’t you start,” Owen snaps, turning on him. Ianto doesn’t even bother to look up from where he’s inspecting his fingernails.
“Going to hit me again?” he asks lightly. [Owen/Ianto]
It Will Bleed You Dry by paperclipbitch - Europe is dying. But Jack refuses to let his team go.
Like There's A Part Of Me That I Want To Get Back Again by paperclipbitch - Ianto Jones, in his crisp pinstripe suit, the remains of a black eye still mildew-green on his face, frowns a little at Owen Harper and says: “Have we met before?” [Owen/Ianto]
No Sense Of Direction by paperclipbitch - After Gwen finally leaves Owen, Ianto is left to try and pick up the pieces. [Owen/Ianto. Link goes to the last chapter of the series, which has links to the previous chapters]
Beautiful Lies by remuslives23 - "Truth is beautiful, without a doubt; but so are lies." Ianto and Jack after the events of the Lost Souls radio play.
Shooting The Messenger by salmon-pink - Jack gives the orders, Ianto obeys, and Owen thinks that maybe everyone has lost their minds, himself included. [Owen/Ianto PWP]
All The Stars In The Sky by lasersforeyes - Sometime after the end of Jack's world, he meets meets someone familiar in an unfamiliar place, and realizes that somehow, things just keep going.
The Dominant Line Between Life And Death by ladyflowdi - In the space of a heartbeat, between the rhythmic pulse of life itself, Ianto’s world is split in two. There is only the Before and the After, the Once Was and Is Now, as if someone has cut him right down the middle, a perfect sagittal seam that has equal parts guts, eyes, and heart. He is coexisting with himself, and the other Ianto won’t stop screaming.
Passing Currents by feathereddino - Gwen assists with clean-up after a case is finished. [This fic is pretty Gwen-bashy/old school fic Gwen characterisation, but the rest of the concept and other characterisations are so fun and spot on that I want to rec it.]
No Word For Yes by copperbadge - Someday he will have a Jack-to-English dictionary. Though it will contain more than just the words, he supposes. And be unsuitable for children.
Life Lived Without Thinking by pocketmouse - While exploring the lower levels, Ianto steps through a doorway, and disappears into blackness. [Owen/Ianto, ish]
Roses In December by remuslives23 - Memories of better times assailed him, snippets of his life ticking over in his mind like flashes of scenes from a film, faster and faster until he couldn't breathe then the floodgates flew open, and he couldn't stop the crippling pain from bending him in two.
Lorem Ipsum by solsticezero - Ianto was going to go home. Ianto was going to take an evening and think about this rationally.
Management Of Dead Bodies In Disaster Situations: A Field Manual by heddychaa - Darragh Edmonds is a so-called "disaster specialist". Called to the site of tsunamis, earth quakes, floods, terrorist attacks, he takes up the grim task of putting order to human remains, and he does it well. Cleaning up after a biological attack on Thames House should make for a comparatively easy day for Darragh: after all, the bodies of Thames House have even been so considerate as to pile themselves right at the front door for him. That is, until he's sworn to secrecy and sent, alone, to collect two bodies from the building's eerie top floor.
Confluence by cmdr_spadge - Once Lisa is dead, it's Owen who decides what to do with Ianto.
Interstitial by sholio - They jostled around each other for a while, bouncing off each other's sharp and broken edges—and then they started to fit, like puzzle pieces that couldn't click together until they found just the right angle. [Owen/Ianto]
do not go gentle by someawkwardprose - His hands were shaking. Lisa was dead. They’d killed her, the whole bloody team, and he hated them. Lisa was dead, and he wasn’t.
Simile by echo - After being trapped, beaten, terrified, and deprived of sleep, Ianto is desperate to get away from the activity surrounding the village. Unfortunately, with a concussion and any number of unknown injuries, that's not really a good idea.
Separated by AuthorInDistress - When the Toclafane attack during the 'Year That Never Was', Owen and Ianto survive that hell together.
C12H22O11 by Jane St Claire - Sometimes things turn up right in the Hub. It's a big time-saver. [A creature falls through the rift. It might be more than what it seems.]
Writing The Truth In Blue by pecos - The glimpse of a pink dress shirt in the rubbish skip was enough tweak Jack’s curiosity. What he eventually found led him to realize what he was about to lose forever.
I also have a number of old deleted classics saved, stuff by rcmclachlan (I just have From Which Come All Things, which is the important one imo), rexluscus, and lawford, and a few others, so if you're an old fan and want those, dm me!