Disclaimer
This is a personal list. Most of my list will probably consist of Nintendo boss fights as that is most of my history. This is also games I've beaten so while I've played and fought many Heartless, I have yet to beat Kingdom Hearts. Also while not all the boss fights on here are magic, I consider Darkness a vague term to begin with. The typing, based off of pokemon, sometimes represents dark magic and sometimes represent evil acts like stealing. I've worked my list around the idea that these bosses are either associated with the night time, or they simply want to blot out the world in some form of darkness or another. If your opinion is different chances are I simply didn't enjoy the fight as much, or I haven't played the game in question. I also only name one boss fight from a series and I consider Marvel Ultimate Alliance and Spider-Man Web of Shadows far different in terms of game series. Thank you.
Links
WARNING possible spoilers WARNING
While not the funniest boss fight ever, Blackheart was a challenge, as after defeating him once, he'd burst out of an environmental object reborn. While this wasn't totally challenging as you just had to kill the destructible objects, it was still interesting and remembered by myself.
The design and boss fight this time around are much better. While Web of Shadows was one of the more unappreciated games in my opinion, it was still fun most of the time, and this fight was pretty fun. Not the greatest boss fight, but not the worst, the design of Mega Venom is still one of the better aspects of the fight itself, though perhaps I have a soft spot for symbiotes.
Part of the elite four in Pokemon Gold and Silver, Karen is a darkness style trainer with her favorite being a Houndoom. While it was safe to have a fighting style pokemon around, it was also somewhat unnecessary as all but one of her pokemon had a second type, and Vileplume was grass and poison for whatever reason.
A recently good Sonic game exclusive to the Wii, the final boss is... actually Dr. Eggman. While there are other final Sonic bosses, none of them are as good as this boss fight, though I must admit, this boss fight isn't all that difficult either. Fun, but not all that hard. Still, nice to see Eggman as a final boss again, as it has been a long time.
Not sure if he counts more as a boss fight or more as a stage obstacle. Still, bringing nightmares to the Bat is not a bad darkness attack in my book, so I'll put him here. Scarecrow in Asylum hits Batman with fear toxin three times in the game, one of which is meant to affect the player, however eagle eyed players can notice the gas before Batman enters an illusion. The third one does have a skeleton brawl at the end of it with a Titan skeleton to face off against as well which is awesome. So far the fear toxin affects... have been less then impressive in Arkham Knight for the most part...
Reaper reaper that's what people call... ehem. Outside of a catchy as hell boss theme, Margeret Moonlight is a twin scythe wielding lolita probably representing the violence in horror media. Also don't get too far away from her as those scythes double as rifles that she can shoot at a good distance. Her design is clever, her boss theme is addicting, and the actual fight is fun, plus there is so much mystery around this character and possible connections to another character in the series, it is hard not to remember and enjoy this boss fight.
While this game was plagued with camera issues and the possibility of having to play the ENTIRE FREAKIN GAME OVER AGAIN because you missed a collectible, this game was really good. The Phantom Blot was beaten, and the day is saved... until you realize that the Shadow Blot was fake and that he was trying to summon the real deal. The real deal is a beast mixing Disney characters Phantom Blot and Chernabog from Fantasia. While more of a stage hazard once more, you have to run around a crumbling castle in an effort to light off several fire works at the beast to destroy him. While he is made of ink, he certainly looks like he is going to cover the world in darkness now doesn't he?
Final boss to my currently favorite Paper Mario game, the Shadow Queen allows you to beat up Princess Peach. The fight is really tough and difficult, and yeah I really dislike Peach for some reason, I'm not sure as to why. Anyway, the design of the boss and dark Peach are awesome, and the fight is really difficult and fun making this the best final boss in the Paper Mario series and probably the most important boss Mario has faced down other then maybe Smithy himself.
This thing is just such a fun fight and such a disturbing fight I had to place it here. The angelic form of the king of all the dark matter from Kirby's Dreamland 3, this thing is an undead darkness mess that is in the middle of being resurrected. And you though Kirby games were cute? This thing bleeds from the eye. Taking the thing down is more like a rail shooter then a platformer much like most of the Kirby final boss fights, and yes it can be very difficult.
My favorite Ganondorf fight is the fight from Twilight Princess and as it stands is tied with my favorite final boss fight in Hylian History... unfortunately it ties with Demise from Legend of Zelda Skyward Sword. Yes you can use a fishing pole in the Ganondorf fight to win easier, but without knowing that, his fight can be tough and difficult, plus there are phases, as you fight him in beast mode, possessing Zelda, on horseback, and then a straight up sword fight. While it may not be the best design of Ganondorf, it is one of the better fights and the better story versions of Ganondorf.
As for Demise, he is the creature that reincarnated into Ganondorf. Demise and his dark version of the Master Sword while not long and has only two phases, it is still a great boss fight. See, you don't need to be stupidly specific in this fight with the motion controls making it more fun unlike other parts of this game. In phase one, the fight is very similar to the Twilight fight with Ganondorf. Phase 2 you are shooting lightning at the foe and literally over powering him.
If this seems like a cop out, it probably is. I apologize for having a tie at the number 1 spot, but since they are both from the same series and both equally as fun for me, this is it, plan and simple. Thanks for reading.