While much more minor and kind of primitive compared to most of the examples here, one boss of Shin Megami Tensei 2 seems to fall squarely under this. At one point you have to get through a shroud of annoying smog to get to Betelgeuse, the boss of the factory area. You are given no information about what Betelgeuse is beforehand, so when you manage to stumble blindly through the fog, find a small out-of-the-way room, enter it, and get immediately confronted with the near indescribable terror that is THIS.◊ What makes it worse is that he constantly chatters his fanged jaw in a two-frame animation, but otherwise is completely non-animated, his horrible eyes staring UNBLINKINGLY INTO YOUR SOUL.
Discovering the truth about Arcadia. And then realizing that this was just an experimental model, and they intended as the final product to have EVERYONE hooked up to this.
That part is terrible, yes. But worse than that? Not even the Archangel Gabriel, otherwise the Only Sane Man on the angels' side, bothers to think what is going to happen with those unfortunates in Arcadia after Gimmel's death, either left to realize just what they've been doing all the time or just rot in the VR chambers, when the Megiddo Arc fires...
Although the greenish-blue YHVH isn't the real YHVH, it's just a facsimile given form and power out of the other three archangels' desire to have their plan for the Thousand Year Kingdom succeed. They're essentially serving a puppet they made, and they don't even know it.
All three Avatars of God are terrifying in their own way, even worse than the Fake YHVH fought in the Center. Sabaoth, Shaddai and Elohim are all absolutely insane Knight Templars intent on firing the Megiddo Arc.
If you're a devout Christian, you REALLY probably shouldn't play this one, as it paints Abrahamic religion with a MUCH harsher brush than any other title in the series - let's just say the local Knights Templar, the Messians, embody the worst aspects of particularly Christian religion, such as the Inquisition and the Old Testament's divine punishments. The real big one for a lot of people is that you have to fight a bunch of Seraphim, as well as God Himself, regardless of your alignment. (Granted, he's meant to be a representation of gods in general, but that he's named YHVH in-game does not help.) How bad is he? Aside from being this huge yellow-skinned... head... THING, he threatens you with a biblical Fate Worse Than Death and makes freaky animations every time you damage him. YHVH nuked Japan just because not absolutely everyone was worshipping him. Or the fact everyone was so horrified at his acts even Satan and the Archangel Gabriel not only give you permission to have a swing at Him, but are even desperate enough to offer to join in in the Law Path?
The fate of Valhalla. Michael, Raphael, and Uriel order Abaddon to swallow it whole in order to get rid of one man, with Cerberus being the only survivor. To make matters worse, Abaddon becomes a Womb Level, and after mortally wounding him, Abaddon realizes he was tricked the whole time. By the Archangel Michael.