Here's my opinions on the 5 darkest Nintendo games.
1.) Majora's Mask... for all of you out there who have actually played the entirety of the game, just pause for a minute to THINK about it. The mask itself was made by an unknown Shadow Tribe (I believe they're referred to as), and it basically turns the Moon into a nuke that will go off in 3 days (let your time run out to see this). I have no idea if you've seen the infamous ZeldaDungeons post about the Stone Tower Temple, but it was a shrine to that mask. When it goes onto somebody, it completely takes them over and gives them dark powers. When threatened... just look up Majora's Wrath, I don't feel like scarring little kids with that image.
2.) Metroid Prime 2: Echoes... That game is straight-up dark. The bosses, the weaponry, the themes, the lore, the everything. It's more of a feeling, so I can hardly describe it.
3.) Twilight Princess... The Dark Link scene alone right after you defeat the third temples' boss gets this on my list. Puppet Zelda and the Shadow Beasts, along with the Realm of the Twili itself don't help this situation at all.
4.) Fire Emblem: Path of Radiance & Fire Emblem: Radiant Dawn... Technically, these are two separate games, but in my mind they are a coherent whole. I won't go on too long of a rant about this, but come ON. Regularly in Fire Emblem, brigands attack small towns and burn them down. In this game, that is the theme of the first chapter is preventing houses from being utterly destroyed by brigands. You don't even have the chance to stop one of them from being destroyed. Then, before the 8th chapter, you see a very detailed, emotional cutscene in which Ike's father is killed by the Black Knight (see my profile pic
). Soon, you learn about the Beorc, and humans, and the Laguz, referred to as sub-humans. Ike finds that the Laguz are great despite all the prejudice about them, they're just like people, so he decides to go to war against Daein with Laguz at his side. Oh wait, I forgot to mention that Daein violently murdered all but the Princess of the Crimean Royal Family within 5 chapters and then attacked you at your base, which is why you had to flee. Skip forwards to the end of the game, and you find that the mount of the Mad King Ashnard was actually the lover of one of the two Dragons you can get as an ally, but he STILL gets killed. Quick look at Radiant Dawn, where the "Dark God" is actually the good guy and you get screwed over left and right by the Goddess Ashera. Plot twist, anybody? The game has a scene where somebody who you're close to is about to be hanged, and another where they show the war. You see the Laguz General Skrimir get nearly killed by the General Zelgius, and watch the devastating effects of the Blood Pact on the newly liberated Daein. Daein and Dae-out, as my brother would say, there is murder, espionage, treason, racism, suggested sexual themes... the list goes on and on.
5.) Final Fantasy VI. Kefka Palazzo, I rest my case.
Honorable mentions include Pikmin, EarthBound, and Fire Emblem: The Sacred Stones. I can't say that I've played through the pre-Rekka No Ken FE games, so I can't pass judgment on them, and Awakening was childs play. Honestly, my least favorite FE to date was Awakening.