I'm going to list my favorite boss from most of the games along with an elaborate reasoning. Don't worry, it won't be all just a bunch of useless junk.
Legend of Zelda: Definitely Manhandla. Manhandla was a cool boss, it was a moving plant with four claws that shoots out fireballs. Is that not awesome? The battle starts off nice and easy, dodge a fireball here, slice up a claw there, but then you take a claw out and the speed increases and fireballs become more frequent. At that point you're all like "Oh, man. I'd better think of what to do, I'll get killed once there's only one!" So then you go up, slice up a claw, then run away before he plows you down. The battle was a mix of timing and dodging, and in that game a lot of bosses are very simple. Manhandla was pretty easy to find out how to defeat, but was still a challenge. I would say Gleeok, however, he's just stationary. The only thing moving is his heads. He's a hard boss, but would be better if he was moving and you had the element of dodging his body instead of just the fireballs that he shoots out. Although, that might make the battle impossible.
Adventure of Link: I haven't gotten very far ... :embarrassed: I've only battled Horsehead and that battle was just too hard. It was slash at his head in hopes that your trajectory doesn't accidentally land on top of him. He hits hard enough where if you don't time right and move accurately, you're going to end up getting yourself killed when trying to attack. I'll have to play through that game and get better before I can give an accurate opinion.
A Link to the Past: I haven't played that game recently and never got super far many times, but I have beaten it. I'll say that the only boss that I can remember that I really enjoyed was Helmasaur. The battle had multiple elements, dodging, smashing, slicing, and stage hazards to top it off. Sure the hazards weren't very frequent and were in an area you probably wouldn't go on, but still, it was cool. The swinging tail that you had to avoid as you smashed up his mask made it where you had to be careful about attacking him. The slicing was fine, but then you threw in the fireballs to make it tough. It's a hard battle, but it's still really enjoyable.
Link's Awakening: I haven't gotten very far in this game either. I've only been through three dungeons and can only remember the battle with Moldorm, which I didn't like. It's like the battle with Moldorm in a Link to the Past, only slightly easier. If you happen to be pushed off the edge, the entire battle has to restart. I can't count high enough for the number of attempts I had to make for my first playthrough that game, but I know it was a lot.
Ocarina of Time: This is a game we all have very fond memories of and I'm not excluded. I've actually got a couple of favorite bosses. The Phantom Ganon boss is probably my favorite. It wasn't hard, but it was fun. The painting portion was extremely unique and something I would have never thought of. The whole guessing which painting he's in was only tough if you weren't quick enough to dodge his attack if you guessed wrong, but was still clever and fun nonetheless. I always love the ping-pong portion of battles in 3D games, 2D games just aren't the same. The whole timing thing about it ... ah, I love it!
Dark Link. Enough said, amirite?
Bongo Bongo's battle was insanely fun. He had multiple attacks that had multiple ways to dodge, his drumming made the battle harder as you couldn't do some of your attacks very well or accurately, along with the fact that you basically needed the eye of truth on the whole time makes this a very conservative battle. At that point, you probably had a lot of hearts, so it wasn't really hard as much as it was just kinda difficult to dodge his attacks while still attacking back. When I first played through, I just used the bow, so I played the safe way. Now that I'm more experienced, I'm trying some more dangerous methods which makes the whole thing tougher. Ah, the battle's just so amazing and the whole concept behind this boss is awesome.
I loved the Ganondorf battle, although it wasn't very hard. He again had the ping-pong portion that I loved and it was really fun. The more times you hit him, the faster the ball became, making it pretty difficult to deflect it back. Then the having to quickly jump over to slash him up made it a lot of fun, although normally I just use the Hover Boots to walk on over
The portion when he's charging up that insanobeam attack was very, very intimidating when I was first playing through the game, but now that I know he's vulnerable when charging, the battle doesn't really have the special "flair" then. It was much more fun when I didn't know of that "cheating" method. Now it's hard to not use that.
Majora's Mask: This game was amazing in a lot of areas. It didn't have a lot of dungeons, so in turn didn't have a lot of bosses. I did like almost every boss in that game. Goht has to be my all time favorite boss in Zelda history, every, though. Everyone loves to roll as a goron, so that just makes it amazing to start off with. The battle is always exciting and dodging his boulders that fly off makes it kinda difficult when closing in on him to attack. The part where he turns around and shoots lightning bolts frustrated me a bit, as I was almost always hit, but now I can dodge those pretty easy. I've replayed that boss more times than I can count, but it's always fun. Now I can beat him in about 2 minutes, so it's not a lot of fun anymore, as the battle's so short, but it's still pretty fun.
Haven't played a lot of OOX, so I can't give an opinion on them.
Wind Waker: I didn't really love any of the battles in this game, to be honest. Most of them were reused concepts and didn't feel very fresh to me. Most of the bosses had very obvious methods of defeat, so it wasn't very fun. The battles I did enjoy were Phantom Ganon, for previously listed reasons, and probably Gohdan. Gohdan was a similar battle to Bongo Bongo in many ways, so it sort of has that sort of thing. You're being attacked from just about every angle and have to take out multiple objects before being able to attack the main portion of the boss. You have to use a lot of your arsenal which I always deem a plus, so that's always good.
Minish Cap: Although one of my top 3 Zelda games, it had really bad bosses. I did like the battle with Mazaal, though. It was basically just Gohdan in 2D, but was still just as fun, if not more. I don't know, but just having it in 2D made me enjoy it more. I'd never think you could utilize the Mole Mitts in a boss battle, and the way they used them I thought was very clever.
Rereading this, it looks very sloppy. I'll have to fix that later, as I don't have much more time, but I'll be sure to do that.