Sequel to Twilight Princess, where Link goes on new adventures - first as Zelda's secret agent, and later out of his own desires. Although it hasn't been updated in a long while, the first two (out of three) parts are complete.
I always think of this fanfic if anyone ever asks for evidence that fanfic can be well-written, and perhaps even surpass the canon material. The nature of the Triforce and what it does to its bearers is explored in a highly engaging and convincing manner, and the characters Link meets along the way are generally nicely developed in their own right. (I don't much like the Traveler, but that's another topic.)