Gundam/Nightmare Fuel

For a Long Runner of a meta-series, the Gundam franchise has loads of really scary moments.

Gundam 00

 * To some, Ali al-Saachez from Gundam 00 is absolutely terrifying. The thought of anyone being so cruel and doing horrible things just because he can, and wanting war to continue endlessly because he enjoys it.
 * "To some"...? To anyone who learns his name!!
 * Don't forget Hallelujah, who is just as terrifying as the Bloody Ali. Ribbons Almark and his Innovator minions - including Nena Trinity - are just as terrifying.
 * The Movie gives us the ELS. The silicon-based organisms themselves are a little unnerving, but it's the way they assimilate other lifeforms that's so terrifying. Silvery crystals grow through the victim (not on, through), in a manner surprisingly similar to the Festum.
 * Particularly harrowing is the fate of, trapped in the cockpit of his mobile armor, as we see the crystals growing out of the skin of his face (even coming out of his mouth), until they shatter his helmet, all while he screams in fear and pain.

Gundam AGE

 * The Unknown Enemies in Gundam AGE, whose sole purpose is to kill and kill and destroy everything in their path, not to mention blowing up an entire colony, killing millions and making millions homeless, in the fashion of Ali Al-Saachez along with the other known complete monsters in the Gundam franchise. This also causes a revenge fuel in the main casts of the show.
 * Thought the big twist revealing that the UE  would make them much less horrifying? Nope, it actually makes them worse. Think about it:
 * And their ace in the hole? Desil Galette. A Deliberately Cute Child who was always bad news to Flit, he reveals his true colors in Episode 13 as an Ax Crazy Complete Monster. From killing his own comrades to, Desil has cemented himself as a horrifying villain in the series.
 * One episode after that,
 * And now we see how far his sanity slipped between generations. He's no longer a Deliberately Cute Child, he's now THIS. In short, he gets worse.
 * Gundam AGE probably wouldn't have its own folder in this Nightmare Fuel page if it weren't for Desil being such a one-man horror show. Yup, he's JUST THAT SCARY.
 * Heck, you can thank Desil for starting a Nightmare Fuel page for the entire franchise.
 * Imagine being chained to the cockpit of a UE mobile suit as an Ax Crazy Blood Knight controls the functions of that mobile suit. Then, when you see your loved one on the battlefield, the system controlled by the Blood Knight orders your mobile suit to open fire on your loved one against your will. And all you could do is watch in horror.
 * Grodek getting jumped
 * In Episode 26, Flit reveals his trump card, a Kill Sat known as the Photon Ring. Much like the GENESIS, it vaporizes any unprotected Vagan that's in its path. Combined with Flit's eternal hatred of the nation that killed both his parents and and... well, you do the math.
 * In Episode 27,
 * Flit's coup d'etat in Episode 28.
 * We witness in Episode 30

Other Horrors

 * Just think of the colony drops - utterly evil and terrifying. Imagine having one colony flattening you right from above your head.
 * And if one colony doesn't do it for you, the opening scene of Gundam X gives us the sight of DOZENS of colonies crashing to Earth, causing pretty much The End of the World As We Know It.
 * No matter what the intention Tomino might have, the monotone "La" during Lalah Sune's attack on the Federation fleet in Solomon is absolutely terrifying, echoing an unspeakable horror Zeon's Newtype soldiers unleash. If one doesn't feel it, one has quite a numb nerve.
 * In addition to the monotone, the original series shows another two bottles of nightmare fuel in the Battle of Solomon. First, the Solar System, the Earth Federation's solar reflector array, Solar System, fires a giant beam that decimates the main gate of the fortress as well as all the Zeon units that attempt to sortie there, burning them into ashes. Then, Dozle Zabi's Big Zam retaliates, frying the Federation fleet in the same way.
 * G Gundam is not short of this, either! Just think of the DG cells and the Devil Gundam. The Gundam Fight itself is one that comes even before DG cells; while the Neo colony nations fight each other using Mobile Fighters for the control of Earth, the Earth has to suffer in silence the property damage and the loss of lives. The message implying the upcoming 14th Gundam Fight at the end foreshadows more catastrophes to come right after the destruction of Devil Gundam.
 * Gundam Seed has the Cyclops self-destruct system (a high-powered microwave weapon) and gamma ray Kill Sat GENESIS. Microwaves heat water, and given that the human body is about 60% water by weight, you can imagine what it does to people caught in its area of effect. GENESIS is basically The Same but More. When it's fired into the Earth Alliance fleet in episode 48, you get to see the crews of the ships screaming and writhing for about a second, as their space suits expand and pop. It's even worse when the weapon hits an Alliance lunar base, as we get to see several Bridge Bunnies at their communications stations, clutching at their chests before blood sprays from their mouths and nostrils, and then they explode...
 * And that's without getting into just how terrifying the leaders on both sides are. Or who is one of the most chillingly realistic Omnicidal Maniacs ever presented by a TV show.
 * By the furthermost extension, all weapons in the franchise, including mobile suits, battleships, and even the heroic Gundams themselves, are a Nightmare Fuel. One professor even states to Alfred in War in The Pocket that they are Necessarily Evil, and are never meant to bring people happiness. Mobile Suit Gundam MSIGLOO even shows us in one episode what it feels like to be killed in the hands of the White Devil and by extension how dreaded Zeon soldiers are in hearing about this infamous name.
 * The "". Seriously, take a good, hard look at the classic Gundam faceplate. Pitiless, merciless, glowing eyes, that V-fin making it look angry... seeing that staring you down in the middle of a fight would not be pleasant, and has utterly terrified more than one enemy pilot in the series.