Bongo Bongo had great build up to me, it was the only boss that really felt like a threat, given it escaped from the well, attacked Kakariko, and escaped into the Shadow Temple, as opposed to being a monster just waiting for Link. No other
OoT boss has quite so many theories about the backstory of the boss, nor did any other boss (save for Twinrova, which I also enjoyed, them playing a role larger than a typical boss) have any role in the game that wasn't text only (you know Volvagia captured the Gorons, you know Morpha drained Lake Hylia, but nothing is seen beyond the boss battle).
Though based on gameplay alone, Ganondorf would win from me. But Bongo Bongo is just so interesting, he's my favorite.