I don't love Dark Link himself as much as other people do, but he was still my favourite mini-boss battle, but not because of him. Rather, it was because of the setting.
When I first played the game, I went into the room he was in and I was confused as all get out. I was inside, yet I was outside. It was a really surreal appearance, especially with the door on the other side of the room just sitting there. It was bizarre, and I became extremely wary of just what was going on. I remember just standing in the doorway at first, afraid to move because I knew something was wrong.
Then I searched out the room, and there was nothing in it. After awhile, I must have hit that correct spot to be to call Dark Link out, and suddenly I was being attacked. The battle itself I didn't find too special, he was fairly easy to defeat, but the whole setting just impressed me. It's one of those very memorable locations in the series.