The loneliness of the areas can get to you; aside from monsters or NPC escort missions, you're the only one there.
Dark Falz. "Hey we finally beat the game! Good job gu—WHAT THE HELL IS GOING ON!?"
When you enter the Dark Falz's lair, all you see is a pretty blue sky and green grass. It seems you have beaten the game and about to collect your spoils, but no, the sky turns black and the nice green grass warps itself to tiles of screaming faces. Then Falz shows up. . .
And just in case you didn't notice, your battleground is covered in twisted faces, writhing in agony.
Just to add to the atmosphere, oh god, the music. The first thing you hear when you warp to the field is The Nearest Place to Heaven. Well, hey! This is kinda nice. Little piano music and birds...why are the birds obviously looping? Must be a lazy track editor...is...is it making a noise? Like a...hazy sorta, distorted noise in the background? And then all the eeriness just adds up over each other and you start to feel real uneasy. Just go near that obelisk and—oh dear god, what the hell is going on. When did I start playing Silent Hill?! W-what are these things?! Why is the music crying at me? Then Dark Falz shows up. The music transitions wonderfully into a grungy sort of techno perfect for a final boss. But it's okay, you beat it! Let's tackle Hard Mode. Ha, beat him agai— what is this, I don't even. You finally realize this just isn't a big monster; that music? That look? You are fighting a god. The tracks in all just work wonderfully at emulating exactly what you're all ready feeling.
The Seabed in Episode II and the Apocalyptic Log contained within. As you move through the dungeon, the logs cover the mutation and corruption of Heathcliff Flowen. Then, you encounter a log entry that's just heavy static interspersed with rambling nonsense. Only the next time you get to speak to your NPC guide, she nervously informs you that it wasn't a recording; it was a transmission from elsewhere in the facility.
Just the name of the final boss arena is somehow disturbing on a very subtle level: Test Subject Disposal Area.
In Episode III, it's revealed that the players really are beating Dark Falz and Olga Flow over and over again, with them getting stronger each time, and eventually strong enough to break free of their confines and destroy everything with no one capable of stopping them.
Anyone who's played Phantasy Star Online 2 need only hear three words before they start freaking out. EMERGENCY CODE: AVOID.
To clarify: When the Avoid Code triggers, you're left with no choice but to run from a flying Eldritch Abomination called a Gel Wulff that can only be described as a giant, ghostly pitcher plant with bat wings. The creature is completely unkillalbe, can move faster in a straight line then the players, and can effortlessly pass through walls. It's only purpose is to hunt down the player characters one by one, and will not stop until it succeeds, or the Avoid Code's timer runs out. It also hits like an unholy eighteen wheeler, two-shotting or possibly even one-shotting a player.
Updates have, thankfully, mitigated the nightmare factor of this Emergency Code: the time limit for the Code has been shortened, and the monsters can now be killed with charged photon turrets.
Official service recently added in Visbolts, blasts of red lightning that can appear out of freaking nowhere and have a fairly-sized AOE. You constantly have to run around to avoid them, which can easier said than done if you're hanging around with a full party or three, as there can be multiple targets for the Visbolts at once.
Something that's also been around for a while is Emergency Code: Destruction that spawns a bomb called a Baize. It starts off as a tiny ball composed of D-Arker veins, but it very, very quickly grows to massive size and eventually explodes. Failing to destroy it in time - which is hard, because it's durable - will cover the affected area in a red hue while some evil version of Acid Rain pours down and drains the health of anything there like mad; it doesn't last forever, but still for a while. If you don't think you can destroy it in time, get the hell out of the area.