There aren't many to choose from, but the Dark Link miniboss in Ocarina of Time is one of my favourite fights in the entire game. I think it's a very well designed fight - Dark Link's opacity and aggressiveness increasing the less health he has, him copying your moves, and his maximum health depending on how many Heart Containers you have are nice details that I think really add to the encounter. There are multiple ways to tackle the miniboss too - you can cheese him with Din's Fire, outrange him with Biggoron's Sword, break through his guard with the Megaton Hammer, use Deku Nuts for stuns, or just use the Master Sword for a proper duel. Fight him with many hearts and you'll get an extended duel, but try it in a 3-heart challenge and you get a shorter, more intense battle. I like miniboss and boss battles where the player can be creative and use different strategies, instead of relying on a specific item or tactic to win. The Dark Link duel is fantastic in that regard in my opinion, and remains one of my favourite minibosses to this day.