Part 6 takes us into the top 40, which has an interesting mix of a few final bosses and a few first bosses. There's even a miniboss! This also brings us firmly into the territory of very good fights. I might still have an issue or two to complain about, but they're hardly held back by those flaws.
40. Dharkstare (LBW)
LBW has perhaps the most inconsistent bosses of any Zelda game, and despite having three bosses right at the beginning of this list, including my least favorite boss of all, it also has another three that placed in the top 40. The first of these is Dharkstare, the remix of aLttP's Kholdstare, which transforms the frozen eyeballs into a frozen sea anemone-thing. The design doesn't make a lot of sense, but thankfully the fight is solid mechanically. You're trying to hit Dharkstare with the Fire Rod, but it's getting in your way with patterns of lasers that Link will need to jump over and later mixes in snowballs as well.
39. Diababa (TP)
Twilight Princess sure takes its time in getting you to the first boss, but it delivers once you're finally there. Like most TP bosses, Diababa has two distinct stages. In the first, you need to use the Gust Boomerang to bring bombs to two massive heads while also dodging occasional biting attacks. Once you've hit both heads, you've won! But not really. The swamp starts to bubble and suddenly both heads are back, along with the massive central body. The main mouth can launch an acid spray attack to mix in with the smaller heads lunging bites, and your helpful bomb plant is gone!
You need to survive a few rounds of attacks to trigger the appearance of Ook, a now-friendly miniboss from earlier in the dungeon. OoK grabs bombs from offscreen and ziplines across the acid swamp while carrying them. Now your challenge is to target one of those bombs and part of Diababa before Ook swings off screen, and you still need to watch out for Diababa's attacks. Knocking out all three heads twice is enough to win. It's a very unique fight with several different fun surprises, and it even puts up a real fight despite being the first boss. My only criticism of this fight is that, on Wii especially, targeting Ook's bomb and a Diababa head quickly enough can be more frustrating than fun. Sometimes it feels like you should've gotten a hit when you don't, and other times you get interrupted by an attack just when you'd finally lined everything up. It's still a very good fight, but that issue holds it back.
38. Dongorongo (PH)
Dongorongo is Dodongo again, but now with a twist that makes the fight actually good. Link is trapped on the far side of a quicksand pit, making direct attacks impossible. Instead, you take control of a friendly Goron and have to dodge Dongorongo's fire breath to deliver a few rolling attacks. Doing so will knock the beast off balance and allow Link to draw a path to bring a bombchu right into its mouth. Dongorongo is never a real threat, which is what keeps this from being higher, but it's always nice to have an ally in a Zelda fight and there's nothing else in the series quite like this battle.
37. Evil Eagle (LA)
The final Link's Awakening fight on this list pits Link against a giant eagle at the top of a narrow tower. You need to dodge swooping cross attacks and barrages of feather missiles while sneaking in ranged and melee hits. The real strength of Evil Eagle, beyond that fighting an eagle on a tower in the clouds is cool, is that it's a late game boss and almost all of your items can be used against it in some way. This fight allows far more creativity than your standard Zelda boss, and you'll need that since it also takes place on possibly the smallest space of any boss in the series.
36. Gleeok (PH)
Phantom Hourglass also managed three top 40 bosses despite how much I rag on it, but the last of them won't be showing up for a while. For now, we're looking at Gleeok, a two-headed remix of a LoZ boss. Gleeok makes lunging attacks at Link and can flood the entire arena with icy water full of hazards, but it's actually another tennis match. A very unique one this time. Instead of batting back Gleeok's attacks with your sword or another item, Link needs to draw connections between the four poles in the arena to create reflectors that will send Gleeok's shots back. It will attack and destroy the reflectors if you put them out too early, though, so you have to be careful to create them just before Gleeok starts to shoot at you.
35. Vaati (FSA)
Vaati is the penultimate boss of FSA, but he ranks well ahead of Ganon. Despite starting with a relatively boring tornado bomb section, the rest of the fight makes the best use of the GBA screen in this game. One phase requires you to use a cannon buried under the arena to fly into the air and launch dive bomb attacks against Vaati, while another sees a miniature Vaati form chase you into that sub-arena. The rank for this battle comes almost entirely from those GBA sections. There's still one FSA boss left, but Vaati best represents what I was hoping the game would be.
...Except that co-op is still basically irrelevant, but, well, that's FSA for you.
34. Vaati (FS)
The second Vaati on this list is the original. Back before Vaati had a human-like form, he was the Wind Mage and the Big Bad of Four Swords. This Vaati is a many stage fight, opening with a challenge to throw bombs into his tornado, moving into a phase where you need to dodge a wheel of minions to get sword hits in, and finally proceeding to a rotation of remixes of the game's other four bosses. I love this as a concept for a final boss. So why is it this low on the list?