My favorite enemy is probably the Iron Knuckle from OoT. You couldn't flinch him, and he took four hearts away from you in one hit (ahh, the good old days when Zelda enemies could do more than a half heart worth of damage). But then they nerfed him in MM by giving half the health, and just removed the Iron Knuckle from post N64 Zelda games, perhaps in favor of the inferior Darknut.
The Garos from MM were another favorite that hasn't appeared since the N64 Zeldas.
Other favorites include OoT Stalfos (by far the best incarnation of Stalfos), MM ReDeads, Bongo Bongo, and OoT Ganondorf.