I think the real winner for gut-wrenching angst in Naruto fic has to be 'self-sacrifice taken to a literal extreme'. Not just dying for the village, but the slow erosion of self for a cause that might not even care. Naruto giving up his identity, his dreams, everything that makes him him, to become the perfect Hokage tool—that stuff gets me. A fic I read had him so detached from his own emotions after years of suppressing them for diplomacy that he couldn't even recognize Sasuke's return as significant. It's not about big tragic deaths; it's about living a life that's a tragedy.
Runner-up is 'survivor's guilt' done through Team 7 lens, especially Kakashi. The man's a monument to lost connections, and fics that explore him watching Naruto and Sasuke head down paths mirroring his own lost comrades, feeling completely powerless to stop the cycle—that's potent. The angst isn't in crying, it's in the empty apartment, the cold meal for one, the mission reports filed to an empty office.
Less common but brutal is 'ideological betrayal'. Sasuke believing so utterly in his revolution that he must systematically destroy every bond he ever had, including the one with Naruto, not out of hatred but out of a twisted, loving necessity. That's a special kind of heartbreak.