One of my favorite enemies would have to be Ghirahim from skyward sword. Not only is he weird and unpredictable, he is really full of emotion bringing his personality to life. That fact makes fighting him really fun.
Darkhammer in Twilight Princess (don't know if Mini-Bosses count) but he's so hard, he's the hardest enemy (in my humble opinion) in the whole of twilight princess for me, and I ALWAYS take damage when I fight him. He's always a challenge, and when he is destroyed it gives me more satisfaction than killing Iron Knuckles, Stalfos or Moblins. Plus, the Ball-and-Chain sweetens the whole deal. The battle itself is great because of the narrow corridor, leaving practically no room for error, and the ability to clawshot to the ceiling to avoid being hit (narrowly) had a certain quality to it, it's indescribable - Moments of panic, fear and thrill in the best possible ways.
That being said, I also hate Darkhammer. It is purely because of him I can't do the 3HC in TP, haha.
My favorite enemy is the Lizalfos. Why? Because I have a weakness for lizard/dragon type enemies I suppose. They are more sophisicated than the standard keese or deku baba, they have intelligence and could easily be a race with a society structure and backstory. My favorite design of the lizalfos is the skyward sword lizalfos. It is so funny to see them mock you hiding behind that huge arm armour thinking they have nothing to fear. The aeralfos from twilight princess is my 2nd favorite.
My favourite is the Keese. They've made an appearance in every Zelda game (with the exception of Zelda II), and throughout the series they have appeared in many different variations. The normal Keese is a true classic, the Fire Keese and Ice Keese were great additions to Ocarina of Time when it came. And now with both Thunder Keese and Dark Keese in Skyward Sword, there is no doubt for me that I like the Keese the most!
Throughout my years of playing these games, i have gown fond of a few things within the entire series. With each game there are enemies that challenge "Link"(myself) and Bring out my heroic side. Each enemy i have taken out has left an impact on the way i play the games and when they reoccur with new ways to defeat them, it just sends shivers down my spine.
My favorite enemy is non other than "Darknuts". In the original all you had to do was stab them in the butt a few times to defeat them. With each new game they're in, there are new ways to defeat them. In Windwaker (my favorite version), you were able to take out their armor piece by piece. You were also able to do neat tricks to avoid them and reach their exposed rears at the same time. In Twilight Princess they took it a step further, When their armor was knocked off of them, they threw their sword at you and used a smaller more agile sword. I know they're in quite a few other games, but the console versions just made them more fun. Not only are they fun to beat, they look awesome.
I like Octoroks ctorok: the best. They were originally land enemies, but as the series progressed, they moved to the sea, too. My favorite version would have to be the ocean ones from Phantom Hourglass.
The Darknuts from The Wind Waker have always been my favorites. I like them because it feels like you meet a skilled enemy, if they lost their sword they just pick up another weapon or use their bare hands. Plus, the battle in the Tower of the Gods was amazing.
I like Gannon from A Link to the Past. Specifically from A Link to the Past. Any true Zelda fan would know this famed misspelling of Link's mortal enemy. So here's to Gannon with two n's, he's my favorite enemy in the Zelda series because with that extra 'n' he shows how bad the translators can be especially for an SNES game that came out in 1991. A rather different choice to pick here, but I like to think outside the box.
My favourite Zelda enemy is Darknuts. Especially from Twilight Princess. I like how you had to destroy their armor first and and then defeat him while you're dodging his sword. I used the back slice and the great spin a lot on them
They're only available on the 2 DS Zelda games. They're almost cannot be defeated in Spirit Tracks. Also, it has many types and each of them have a special ability depends on its type. I just love when I defeat them. xD
I thought the Garo were the coolest enemies in Majoras mask, but the Garo master was just so fun, epic and had that difficulty to it which other enemies lacked. Whats' better than a masked ninja in a purple cloak with two flaming sword that can teleport and he drops out of hell...