Mother Brain - Super Metroid
It's hard to explain why it's so great without spoiling it for those who haven't played the game yet, it's something to be experienced.
Metroid Prime - (title drop)
Pretty intense fight overall, you have to constantly switch your beams to fight Metroid Prime while avoiding it's projectiles and rush attacks and finally Hypermode it to hell the Essence mode.
Ornstein & Smough - Dark Souls
The reason people fear Arnor Londo, and the reason you will die, a lot.
The Boss - Metal Gear Solid 3: Snake Eater
Not only do you have to prove that the student has finally become the master but you also have to do it before some MG-21s fly in and bomb the place, with the song, "Snake Eater" acting as your timer before they arrive.
Liquid Ocelot - Metal Gear Solid IV: Guns of the Patriots
The final fight to conclude the Metal Gear Solid (1-4) saga, complete with music, effects and animations from all four games, a pretty great way to wrap up the original pre-MGS V Solid series.
Bowser - Super Mario Bros. 3
It's short and sweet and to the point, it's definitely not too complex but it's a fun fight.
Mundas - Devil May Cry
They really went all out with this boss and it seriously feels like it's never going to end as when you get to the end of one crazy section another one begins. It's a great rush and it ends off the game quite nicely.
