MechaUltimaZero wrote a few that I thought were pretty interesting, although they're both Dead Fic and only one or two chapters.
Oathkeeper: Wherein Link refuses to return to the past so that he can keep the promises he made during the game (mostly related to rebuilding Hyrule, but also his engagement to Ruto).
Monstrous Might: Dark Link is even more of a reverse Link, being a Large HamCard-Carrying Villain of a Complete Monster who borders on being a Motor Mouth... and who promptly murders Link and hijacks the plot to become a Villain Protagonist. From his perspective. Also an In-Universe deconstruction of the idea of Link being a player avatar.
So do I, actually. Although Malon's feelings are made a lot less ambiguous in the manga, she still doesn't admit them IIRC.
My favorite pairings, though, are Link/Navi and Link/Tatl.
After reading Oathkeeper again, Link is a little speech-prone, but it looks to me like about half of his dialogue is normal.
You check out Monstrous Might?
I was trying to come up with Link's ultimate equipment. Using different stuff from all his different games. I can't decide if he will look ridiculous or completely awesome and Bad Ass and what I'm using for like his armor for when shit gits real. Using both Canon information supplemented with a bit of fandom.
Tonic: Magic armor mostly unchanged from twilight Princess but I might have it not drain rupees just to wear it only when taking a hit.
sword: the great fairy sword. I'm going to make it is second strongest sword for brute strength *
trying to engineer a reason for him to sometimes find the biggron sword better from the situation
however magic energy extends from it and sword beams charge quickly and are much stronger from it.
shield: the Goddess Shield, this one is also the mirror Shield it reflects things and just having it equipped maked Link take half as much damage even when he failed to defend with it.
Boots: Pegasus boots, there are going to be based on what I thought I would be receiving in skywards sword instead of the double hookshot. Not that I don't mind them. Link runs twice as fast normally and during a Sprint with them, furthermore a Sprint is twice as long and he can defy gravity during one. And just run over the air or water.