Okay...I have a number of them. I'll explain why, so don't worry. So, in no particular order...
Nyarlathotep - He's been in a number of places, but he is the true evil behind three Persona games, either in the background or the active end boss. The Crawling Chaos of a thousand different forms was the manipulating force behind the normal villain of Persona 1 (Kandori), supposedly acting as just the man's Persona...but really eating away at his subconscious. He then took a more aggressive role in Innocent Sin and it's deja vu sequel, Eternal Punishment. Doing what? Oh, nothing... Just destroying the world TWICE. No worries. All the rest...I think anyone who knows HP Lovecraft knows why Nyarlathotep is an incredible evil.
Sephiroth - From FF7, of course. The fandom fights between Kefka and Sephiroth are aggravating. Kefka is alright, but he is a rather foppish genocidal clown. You can't fear a guy who's always been insane, even with all that power. As the hero, you can really only hate him. Sephiroth can be feared for uhh...some good reason. First, he use to be SANE. Up until the Nibel Reactor, he was just the deadliest Soldier in the program. He even laughed and made fun of Hojo. When he learned what he did in Nibelheim, he broke. His disintegration was like the one Cloud went through during the game. And while some might joke about his Norman Bates complex...that just makes him worse. Because mother really IS a part of him... Of course, Cloud nipped him in the bud quickly enough, but you have to give him credit for nearly going all-powerful and ruining the world from inside a chunk of materia.
The Reapers - I haven't played Mass Effect, but I know a good deal about it. Props must be given to Sovereign and the other Reapers. You have to. For the last untold eons, they have set up civilizations up for a major fall, the entire Mass Effect program designed to both kill those who pursue it AND provide power to support and create more Reapers. And after AGES, they manage to finally put a dent in them, those huge and deadly SQUID VESSELS OF DOOM, whose numbers are in...what? The thousands? Millions? Far too many. The scorecard so far is that Shepard has maybe a couple victories too the mass genocides concocted by the Reapers. I...don't see a way out of this Xanatos Gambit. The Reapers basically have the universe by the Jorbloks.
X-Death/Exodus - Final Fantasy 5 has a bizarre tale, in reference to its villain. Let's see here... Our boy here is the consciousness and power of some sort of tree-thing that was the focal point of all evil that could command the power to void matter. This guy is...a deadly black mage that is also part of this evil tree which was sealed away, and then HE was also sealed after pushing into the world, so he was sealed TWICE...and managed to break his prison from the inside by taking over minds and creating deadly monsters, then he destroyed things, tricked the heroes into doing exactly as he wanted to that he could gain access to the void, and then ummm...HE TRIED TO DESTROY THE WHOLE UNIVERSE!! ALL OF IT!!! he was a proper evil villain, card carrying almost.
The Profound Darkness - For those of you who haven't played the original Phantasy Star Saga, here is what the PD is. It's the dark side of an almighty being that split in half and was locked up by the lighter half using the entire Algo Star System. It spent three games using its avatar, Dark Force, to bust its way out of the Abyss. In short, your trials over the first, second, and fourth game are all because this massive abomination wants a breath of fresh air. It will corrupt any being, destroy anything or anyone, and cause all manner of calamities (like the destruction of planets) to get its way. And if not for some artifacts, some powerful spells, and your hardy training for that romp into the Abyss itself, you would be the buzzing of flies in its presence.
Tohru Adachi - Stepping away from the extremely powerful for a moment, I like the cut of Adachi's jib. He spent the whole time looking harmless, even inept. In reality, he's a master of clever ploys and manipulation, and a serial killer besides. Even though he's not the main evil there, he has style and wit, and things wouldn't have progressed as they did without him. Extra points go to him for being voice by Johnny Yong Bosch. I really enjoyed his presence in this game, and playing a bad guy no less!
Deus Ex Machina - Okay, back to super power. YE SHALL BE AS GODS. Deus is a galactic battle system deemed too powerful, too dangerous, and too intelligent to be used. It was going to be dumped. Instesd, it took over the ship, executed everyone who tried to escape, and forced the captain to detonate the ship and send its remnants to an unknown world devoid of intelligent life. Deus is the PLOT. He created intelligent life while damaged and incomplete, made it evolve, tested it, improved on it, kept working at it, and so on. The ten thousand year history of the game, Xenogears, is all his doing...in order to make repairs and leave this place. Everything that happened was to repair and improve what was, to the people, the physical manifestation of god, powered by the Zoher Modifier...a device containing a higher-plane dimensional being. The evil part is that everything that happened, good or bad, is essentially his doing and as your god...HE DOESN'T CARE. Also, he wasn't completely destroyed, but piloted off the planet by one of the other antagonists. No word yet on what the hell happened after.