Not counting Sailor Waddle Dee from Super Star (Ultra), and I guess not counting Waddle Doo from 64 since both of those are PURPOSEFULLY super easy, the boss fight I have come to have the least trouble with is Nightmare (from Nightmare in Dream Land). I've played that game to death and know the fight super well, so it just never gives me any issues.
Side note: I've been posting these exclusively on Tumblr since they've mostly been really simple and relatively effortless, but this one turned out surprisingly well so it's going on other sites too.
Nightmare © HAL Laboratories