Alright, this is a niche I've spent way too much time in. 'Dark Link' could mean a few things—the 'Ocarina of Time' shadow self, the corrupted hero from certain timelines, or even a wholly AU version—so the platform really depends on what flavor you're after. I'm assuming you want the angsty, internal-conflict, doppelgänger-drama type stuff, not just a villainous caricature.
For sheer volume and that classic, deeply-character-driven take, I'd actually point you towards Tumblr first. It's not a traditional archive, but the Zelda fandom there, especially the older crowd, produces incredible meta and ficlets centered on identity and trauma. Search tags like #dark link, #hero's shadow, or #linked universe dark link. A lot of writers cross-post to Ao3, but the preliminary drafts, headcanons, and shorter pieces live on Tumblr, and the conversations in the notes often lead you to the best multi-chapter works. It's more of a curated discovery process than a library.
Archive of Our Own is the obvious answer for a structured collection, but you need to master the filters. Go to the 'The Legend of Zelda & Related Fandoms' tag, filter for the Relationship 'Link (Legend of Zelda)/Link (Legend of Zelda)', and then add additional tags like 'Dark Link', 'Selfcest', 'Identity Issues', and maybe 'Angst'. Sorting by kudos or bookmarks will surface the community favorites, which are often the most nuanced takes. The quality there tends to be higher on average because of the tagging system, letting you avoid the crackier or purely smut-focused stuff if that's not your jam.
The thing is, the 'best' collection is subjective. Some of the most psychologically intense fics I've read are hidden in personal blogs or on FF.net from 2006, written in that raw, unpolished style that somehow makes the horror of facing yourself hit harder. Don't sleep on FanFiction.net's older archives, even with its clunky interface. Just be prepared to sift.