Man, if you're asking for the most popular, you're inevitably gonna hear about 'The Sacrifices Arc' by Lightning on the Wave. It's basically a cultural landmark at this point, this massive seven-book rewrite that starts with 'Saving Connor'. People either swear by it or bounce off it hard because it's such a commitment—like, it reworks the whole magic system and Harry's personality into something way more Slytherin. Personally, I think its popularity comes from how deeply it builds a dark, political wizarding world; Harry's raised by Sirius and Remus, and his relationship with Voldemort is this slow, inevitable gravitational pull. The sheer scale of it, following Harry from first year onward, makes it feel like an alternate canon for a lot of readers.
That said, I know some folks find it a bit divisive. The prose can be dense, and the characterization of Harry is so different from the brash kid we know that it throws people. But for exploring a Voldemort/Harry dynamic that's less about instant romance and more about shared power, destiny, and twisted mentorship, it's kind of the definitive epic. You don't get to that many kudos and bookmarks on AO3 without being the go-to for this pairing.