After beating the game and starting over in "New Game +" mode, right after Crono meets Marle, you can take a shortcut that launches the two of them all the way across time into the final battle with everyone's favorite ancient Cthulhian alien parasite god-monster, Lavos. Some first date. If you survive, you're taken a super secret developer room, where sprite versions of the game's developers brag about their "stunning 32 meg graphics," chat about their favorite sports teams, and give you advice on love. Because game developers would know best.
In three Ratchet & Clank games (Going Commando, Up Your Arsenal, and A Crack in Time), the developers at Insomniac Games slipped in a feature that they called the Insomniac Museum. You can only access it between the hours of 3:00 and 4:00 AM (because they're called Insomniac, we get it) but once you get in, you can see all of the half-formed skeletons of ideas that didn't quite make it into the game. It's sort of fascinating to see how hard these designers worked on features that ended up not being implemented at all. It's enough to make you wish every game came with its own museum.
Silent Hill 2 is a terrifying game that chills the blood and forces its players to question their roles in the vast, uncaring world. So it's only natural that in one of the endings to this horror masterpiece, the player character, James, discovers a secret control room where a happily panting dog has been orchestrating the whole thing. James then falls to his knees and says, "so it was all your work?" The dog licks his face. It's either a silly cherry on the top of an otherwise dreary, depressing game, or it's a middle finger to the players that take these games seriously. Either way, it ends with the dog barking a silly song over the credits, so I think everybody wins.