Don't Leave Me the Way I Am: AU. "He wished he could use Mjölnir as a blacksmith would, hammer himself out until he was shining and straight." DUDE. Listen to me. This starts out iffy, but it grows into such a magnificent fic. It's mostly about a forbidden desire for Loki, moreso than homosexuality. Tons of tortured pining. It also has an incredible sex scene.
Safe and Sound: Post-Thor "They have not called each other ‘brother’ since Svartalfheim, but when Loki gets injured in front of Thor, his reaction is not that of an enemy, or a grudging ally." In which Loki is full of bitter hurt, but Thor is too devouted to him to stop.
Dainsleif: Pre-Thor "Loki has a well-crafted plan to win the powerful sword Dáinsleif. Thor just wants to kill a dragon. Then they encounter a bunch of lustful elves and things suddenly become much more complicated." Really lovely just as a fantasy story, plus agnsty sex.
Trajectories: Post-Avengers. "The Chitauri and Thanos capture Thor to cause Loki the most unimaginable pain. Loki joins with the Avengers to get him back." Surprisingly good action and you can't pretend Thor being Loki's weakness isn't romantic as fuck. It's basically canon, shhh.
Unnamed Days: Post-Thor "Following the events of Thor: The Dark World, Jane opens her home to Thor...As it turns out, Loki has plans of his own..." As in, Lokie 'dies' in Dark World in Thor's arms and supposedly sacrifices himself but at the end we see that he's alive in Asgard. This does have more Jane than I'd prefer but it's MASSIVE so there's a lot of great stuff. I may have cried during the first half. When they first reunite.
A History of Things Unsaid: AU. The Jotun Kings and Princes gain immortality and a ruthlessness unmatched by any other by having their hearts consigned to the Casket. Cue Odin bringing the forces of Asgard to Jotunheim on the day Loki's heart is to be sealed away, and you've got a botched ceremony and Odin being forced to take both the Casket and baby Loki. - It's a HUMDINGER of a sick twist.
My Mother Would Be A Falconress: OK IT'S GEN, BUT IT'S SO GOOD. It's kind of about Loki growing up.