1. Trading Places With the Joker in Batman: Arkham Asylum
When Batman: Arkham Asylum first graced store shelves, it was a revelation. Not only was it that very rare thing -- a great licensed game -- Arkham was perhaps the absolute best superhero game ever made. Sure, there's some debate for and against its sequels, but AA stands out to most as a pretty much pitch-perfect Dark Knight simulator. Not the least important factor being its incredible use of Batman baddies. Joker was the star, of course, but Poison Ivy, Killer Croc, Harley Quinn, and more all got more-or-less their due in one way or another.
Definitely falling into the "more" category was Dr. Jonathan Crane, a.k.a. The Scarecrow. His psychedelic encounters with the caped crusader were phenomenal, and a great change of pace in an otherwise often dreary asylum. Each had its own unique spin, but the one that stands above the rest is appropriately the last. While on the trail of the Joker, the player (and Bats) lose control simultaneously as the game appears to freeze and crash.
An eerie laugh is the only indication that somebody didn't scratch your disc, and suddenly we're whisked back to the beginning of the game. Except that this time the Joker is in control of the situation, and it's Batman being carted off to Gotham's least hospitable hospital.
It was a wonderfully delirious way to cap off one of Asylum's more interesting elements. Not to mention it set the scene for the conclusion to Batman: Arkham Knight years later. A little bit of foreshadowing goes a very long way, as it turns out.
2. Eternal Darkness: Basically the Whole Damn Game
When it comes to games breaking the fourth wall Eternal Darkness: Sanity's Requiem wasn't even close to the first. When it comes to good old-fashioned fucking with players, though, it just about wrote the book.
The game's time-hopping and appropriately Lovecraftian tale was met well by players at the time. However, it was the patented, so-called "Sanity Effects" that made the horrific third-person adventure truly stick out. If not by everlasting quality (as returning players might find today) at least in sheer quantity. At any moment, your character might do something outrageous like accidentally shoot themselves during a bog standard reload animation -- and then everything would reset, as though nothing ever happened.
Besides your traditional health bar, Eternal Darkness equips its many playable characters with a measure of sanity. Encountering the game's honestly somewhat mundane enemies will deplete that grip on reality, and start all kinds of weird shit often much more terrifying than the actual, eldritch entities you encounter.
These range from extra ambience -- like screaming children, bleeding walls, and a slowly tilting game camera -- to the just plain mean. For instance, telling the player their controller has been disconnected, adjusting the game's volume without warning, thanking you for completing the "demo" and even a false "blue screen of death."
They only get more twisted (and often upsetting) from there. Whereas a BSoD is an error mostly saved for PC users, console owners would be much more likely to be fooled by the dreaded Disc Read Error.
We weren't joking about them being patented, either. Nintendo actually filed for the rights to the mechanic, such was their belief in how unique it was. It's only a shame that said patent never got to see the light of day again. Despite a strong fan following at the time, Eternal Darkness never got a sequel from the fun-loving publisher. Too bad, because they really had something going with the ol' "Make You Believe You Deleted All Your Saves" trick.
More than a decade later a spiritual successor from roughly the same team that brought down the GameCube's fourth wall was supposedly in the works. However, given the developers' shady past in the time since -- not to mention their dead silence -- you'll have to decide for yourself if it's likely to materialize.