I've been so bored the past few days I went through this entire thread. Here is every story I found worth reading and hasn't been taken down (RIP Fool's Gold). Some of these may already be in the library. There are library fics that aren't here (The Black Prince).

Library Worthy stuff AKA the 5/5s:
Life and Honor - Jaime goes to the Wall after killing Aerys and kicks off a great redemption arc for him as Mance Rayder's bro and an all around badass black brother.

Wounds - Robert dies after Robert's Rebellion and Stannis is proclaimed King. Heavy character focus on Stannis and a still alive Lyanna Stark that I'd characterize as friendship and mutual respect more than romance.

Scream Against the Storm - Stannis as the Crow's Eye / Bloodraven's magic apprentice. Handles ASOIAF Magic wonderfully, and nothing is ever freely given. Really plays into the whole magic as a sword without a hilt, and is straight up lovecraftian sometimes.

Maternal Instincts - An Elia-centric story where Rhaegar wins the war. She decides the best way to keep Jon from starting a succession crisis is by being nice to him. Beautiful and heart-wrenching.

The False and the Fair - Jon Snow as a girl. It's...hard to describe this in a way that does it justice, but it is quite a good read and isn't afraid to hurt the characters. Not a Stark wank.

Disengagement - Jaime saves Princess Rhaenys and is tasked to protect her when she is sent to ward with the Starks. A great character development pieces and redemptive arc for Jaime.

One-shots:
Reap the Whirlwind - Cersei / Stannis - 3/5
Cloak and Needle - Barristan and Arya road trip 3/5

These are all just Cersei / Ned oneshots. Most of these are similar-ish in idea, but have different executions. Just in case you have an itch to scratch like I do.
The still after the storm - 3/5
We're Only Taking Turns Holdings This World - 3/5
The joinery- This one stretches incredulity and is probably the worst of these oneshots. Author fails to grasp the very basic precepts of politics, and people generally act like morons. Still, it's character and relationship focused, so if you can power through it, might be worth reading on a slow day. 2/5
And Nothing Is Gained By Not Gathering Roses - Interesting, not-quite-romance, that begins at Harrenhal. - 3/5

SIs / OCs
Not Throwin Away My Shot - Alexander Hamilton as Littlefinger before Robert's Rebellion. Has some good political maneuvering in its last arc and handles it better than most. -3/5

Dreadful - Ramsay Bolton SI where he chooses not to kill Domeric. They become bros. However, he also forms a band and the fic takes a lot of time focusing on it to its detriment. -2/5

Rhaegar the Great - Rhaegar SI. He spends a lot of time falling in love with a smallfolk girl and recreating Shakespeare's plays. A decent time-waster. 3/5

HBO WI: Joffrey from Game of Thrones replaced with Octavian from Rome - Octavian as Joffrey. Some Rome wank, some fix-it. Nothing special, but at least doesn't uplift us into guns and canals. He does, however, have a proper Roman appreciation for good roads. 2/5

A Skagossan Tale - SI into a Skagosi during the War of the Ninepenny Kings, although it's not a "Hard SI". More like an OC character having some dreams of our modern society and being inspired to take a different route. Not super hard into the uplift. 3/5.

Climbing the Ladder - SI into Baelish. Stretches disbelief with how well he can invent stuff like better horse harnesses and ships, but at least no canals, crop rotation, or seed drills. Basically ASOIAF if Baelish isn't an asshole. 2/5

Purple Days - Time loop Joffrey. Shitty YiTi arc in the middle that can be skipped. Somehow gives one of the most hated characters in ASOIAF a redemption arc. 3/5

The Everyoung Dragon - SI into Daeron Targaryen (The Young Dragon) during the War of Dornish Subjugation. Written from the PoV of his sister (who wants to bang him). Reads like a slowburn Targ incest, but is surprisingly done well. Good for anyone who hates those Dornish cunts, and likes the pre-canon history of ASOIAF. 4/5

Dragonstone - Stannis has a dragon. 3/5

Stark Fics

To Go Forward - Jon Snow goes back in time. 2/5

Valar Botis - Stark wank 2/5

A Better Fate - Jon goes South, and then through some contrivance misses the war. Some Frey vengeance thrown in. 2/5

Kingdoms at War - Robb / Margaery wank. 2/5

Dragons of Ice and Fire - Jon gets an Ice Dragon. The first arc is probably the strongest bit of it. Once warring with the Boltons and the White Walkers gets underway, it can get a bit confusing what's going on. It's also way too bloated towards the end (could easily cut 2/3rds out). 3/5

Post-Rebellion AUs
Summer Crowns - Robert and co. go east to hunt down the last Targaryens. Start a slave crusade instead. 3/5

Quests:
A Dragon in the North- Jon Snow as a Dragonborn. (How do you not know about this). 4/5

Murder and Iron - ASOIAF / Forgotten reams Quest as Robert's son. 3/5

Ours is the Furious Grinding of Teeth - Stannis Quest that went from exploring the world to becoming King of Pentos. Voters are cunts. 3/5

Ours is the Fury - Robert Quest. Basically fixes Westeros and is unapologetic for being an absolute unit. Can wear you down towards the end. 3/5

Others:
The Dance is Not Over - Set during the Dance of the Dragons. War doesn't end as quickly and Westeros ends up split in half. Recommended if you like ASOIAF historical pre-canon pieces. 3/5.

Times Like These - A Lyanna / Stannis fic. Quite character driven, a bit angsty? 3/5

The Queen That Was Promised - Cersei / Rhaegar where Rhaegar becomes interested in Cersei after she talks to him about Maggy's prophecy. Character motivations are a bit fuzzy at times, but it's still a decent slowburn romance and enough of an AU to be readable. 4/5

Stuff I haven't read but plan to as they come recommended:
Guileless Son
Robert's Rebellion: Writ in Blood
Our Choices Seal our Fate
I was whole, whole I would remain
Rebellion, Treason, and Plot
The Weirwood on the Volcano

 

Proof that having a huuuuuuuge wall won't stop Muslims and bad hombres from coming into the United States of Westeros. SI tries to make Westeros Great Again. Tries. 4/5

 

It turned to garbage after the coup and became like every other SI fic without the uplift, replacing Stark wank with Stark and Baratheon wank.it has lacked any real tension for the past ten chapters or so. 2/5.

 

The Private Journal of Lysa Tully

SI into Lysa when she's 14, before the whole Littlefinger thing. It's...quite domestic, I suppose. Very slice-of-life, and most of the story deals with her relationships with the people around her and Jaime Lannister rather than an attempt to win the Great Game or build C a N a L s. You could honestly almost treat this as an OC Lysa Tully for all that the SI is a device to change Lysa into someone more pleasant / not infatuated with Baelish.

It also has a sequel from the PoV of those around her, which helps flesh out other characters. Sadly abandoned, but it's last chapter was a satisfying enough climax. Jaime and Lysa's developing relationship is believable to read about, and the SI is far from a Mary Sue (there are multiple times when her 21st century morals screws her over and done so in ways I really appreciated). 4/5 I think.

 

I actually found the Private Journal of Lysa Tully from that thread.

It's alright, but with only one chapter out it's hard to say whether it'll be worth reading.