60. Horsehead (AoL)
This is the only boss I actually fought in Adventure of Link, and as much as I'm not a fan of the game itself, I actually enjoyed this fight. Horsehead gets as close to feeling like a melee duel as anything could have on the NES, and it does it while sporting a surprisingly good-looking sprite. The fight is so simple that there's not much else to say about it. Sometimes doing one thing well is good enough.
59. Helmasaur King (aLttP)
Helmasaur King is an amazing fit for its dungeon because it's a giant version of enemies you've learned to deal with on your way to this battle. Presumably it's an angry parent out to avenge all its babies, and it's more than equipped to do that with a dangerous barbed tail and fire breath. This would be just about my ideal boss if not for the small arena and the imprecise methods you're expected to use to win. Bombs and the hammer both work against the Helmasaur King's mask, but neither feels good to use. If this fight had been against a faster King in a larger room and Link had a ranged attack to use against the mask, this might have been top 10. As it is, #59 isn't bad.
58. Gemesaur King (LBW)
Gemesaur King is the latest LBW rehash of an aLttP boss, but this time it comes out slightly ahead. Gemesaur king answers my request for effective ranged attacks and a larger arena, but it makes the bombs so strong that they almost trivialize the fight, and the room still isn't big enough to give poor Gemesaur much room to roam. The fight's best moment comes after you've broken the mask, which eventually causes Gemesaur to cut the lights and transform into a blindingly fast shadow beast that Link can only evade by jumping into the 2D wall. That's almost what I want from this fight. It comes out ahead of Helmasaur for taking steps in the right direction, but it's still not enough to catch more than a glimpse of what this fight could be.
57. Gohma (OoT)
Give Gohma some credit for being first: Nintendo hadn't had to do a 3D boss intro before this, but Gohma's is done well anyway. Gohma passes the dungeon integration test easily: you're told to enter the Deku Tree to fight an invader, and you can see the parasitic work of Gohma's children throughout the dungeon. It earns some cool points for that boss intro and title card, but loses some for being an eyeball with arms.
What really pushes it back to #57, though, is that it's a tutorial boss that isn't allowed to put up much of a fight. Jumping at it with a stick a few times is enough to win. Great bosses probably shouldn't lose to sticks that easily.
56. Crayk (PH)
Whatever else you can say about PH, it deserves credit for making an effort to use the unique structure of the DS in every fight. Crayk's trick is to turn invisible. That sounds unfair, but Link gets the ability to see through its eyes on the top screen, so you can use your view of yourself to locate Crayk and fire off an arrow before it reaches you. This is an amazing concept that, like Phantom Ganon in Ocarina of Time, is let down by the game's slow controls. The ideal version of this fight would probably require something like a Kinect or VR helmet to work, because that would let you slash around in 3D at a realistic speed and let Crayk appear behind you much more quickly.
55. Genie (LA)
I like Genie. With Facade, it's the best representation of a taunting boss in Link's Awakening, and its stupid clown face really gives it some taunting credibility. Even though it's just the second boss in the game, it has a real attack ability in its fire balls, and it makes clever use of the dungeon's item by requiring you to throw its bottle against the wall to deal damage.
So why is it down here at #55? This game had to make some sacrifices to run on a GameBoy, and at the end of the day that means all of its bosses are a bit simpler, slower, and in smaller arenas than I'd like.
54. Angler Fish (LA)
Coming in as the #2 boss in Link's Awakening, it's the one that's a large real life animal. That's okay because angler fish are awesome. You don't need to get creative with a design when evolution already gave you plenty to work with.
Angler Fish unfortunately does not make use of its lure in the battle, but it does cause blocks to rain down on link and has some moderately dangerous dash attacks. The fight gets away with being slow more easily than others in the game because it's underwater anyway, although I still wish they'd found a way to use darkness here. It's an angler fish, for Nayru's sake! That's their whole shtick!