Favourites: (not really any real order aside from the Helmasaur King):
Helmasaur King(best boss in the series. He's big and epic feeling, he's challenging yet fair, he has multiple ways to fight him that suit different playstyles, and he changes things up as the fight progresses. Flawless.)
ALttP Ganon(most challenging and rewarding Ganon fight on a pure gameplay level, unless if the Yuga Ganon fight in ALBW counts)
Yuga Ganon(see above)
Koloktos(such an epic boss that made good use of the whip)
Goht(love the fast paced feel of the fight)
Thunderblight Ganon(challenging fight that pushes you to learn it; feels rewarding when you do)
Blind(great fight in the tradition of Gleeok and Jermafenser from the previous two games; really frantic and fast paced)
Rebonack(great twist on the Iron Knuckles in Zelda 2; feels like a duel)
TWW Ganondorf(while not as challenging as he was in ALttP, his TWW fight is epic, as Hyrule and everything in it is being obliterated around you, not to mention the epic music)
Stallord(the Spinner makes this battle exhilarating)
Monk Maz Koshia(multiple ways to tackle him, and he's a great challenge)
TWW Gohma(coolest incarnation of Gohma in a Zelda game, IMO; epic feel as you swing across the room)
TMC Vaati(the multiphases and challenge with Vaati's gradual transformation are great)
BotW Ganon(yeah, both phases. I like how neat both forms are in terms of appearance as well as the music and fact that the first form feels like a true test of what you've learned, although completing the four DBs can make it a little too easy, and while the second form is easy, the scale, atmosphere and music elevate it to really high levels, plus it feels like a victory lap like the second form of Mother Brain in Super Metroid)
Trinexx(epic scale and multiple phases, along with a decent challenge)
Bongo Bongo(multiple ways to fight him, cool arena, felt epic)
OoT Phantom Ganon(great multi phase fight. Phase one feels similar to Rebonack with a cool twist, and while phase two is derivative, it's still fast paced and fun)
Least Favourites:
Zelda 1 Ganon(pathetically easy, if this wasn't Ganon, you wouldn't be able to tell he's the final boss. He goes down in just four stabs and one Silver Arrow, no final boss music, doesn't really feel epic, just an absolute bore. They improved the Ganon fights from ALttP onward aside from maybe the Oracles, but there he had an actual final boss tune that was decent atleast)
Twinrova(SO. MUCH. WAITING.)
Scaldera(King Dodongo, only worse)
Mazura(basic Iron Knuckles are more active! I know he's the first boss of Zelda 2, but come on...)
Zelda 1 Gohma(one arrow. Really?!)
Fyrus(way too simple; fight is over before you can blink)
Of course, there's other bosses I love and hate, but these are just some of the few.