All spoilers will be unmarked ahead. You Have Been Warned!

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Games:

Five Nights at Freddy's

Five Nights at Freddy's 2

The Puppet shows up in the post-Night 4 minigame. Remember, all of the post-night minigames take place in the first game's pizzeria.

Five Nights at Freddy's 3

The ending of the Night 5 minigame. Having been cornered by the souls of his victims, the Purple Guy panics and tries to hide... inside Spring Bonnie.
Sometimes, when you start the game up, you see... Springtrap. Taking off his mask.
Brightening the Night 6 newspaper reveals something horrifying: Springtrap apparently survived the fire.

Five Nights at Freddy's: Sister Location

Handy on Night Five tells you to look out for two technicians. You find each of them on Ballora and Foxy's respective platforms, dangling from nooses.
As stated before, entering the Private Room and inputting 1983 on the keypad gives you camera feed of the house from FNaF 4. Also, the Golden Freddy/Fredbear plush in the Private Room is holding a walkie-talkie.
If Handy's line that you have entered a "highly dangerous" area upon making it to the Scooping Room doesn't tip you off that something bad is about to happen (he has proven untrustworthy), maybe the discarded and broken shells of both Funtime animatronics and Ballora laying around your feet will convince you. No? What about that tangled endoskeleton rising up behind the window?
The Custom Night ending has one: Ennard fleeing the now rotten, purple corpse... which then stands back up, with glowing silver eyes fading into view in what were previously empty sockets.
The Custom Night Golden Freddy cutscene. Springtrap lives.

Freddy Fazbear's Pizzeria Simulator

An extremely meta example, and the defining moment of the game. At first, the game appears to be a simple 8-bit troll game of the kind Scott is known for, as Freddy throws pizzas to the right of the screen; the fact that it's free on Steam and entitled Freddy Fazbear's Pizzeria Simulator certainly helps with that. Then, on level 4, the sprites begin to glitch severely until the screen goes black... and fades back in to reveal an extremely damaged Baby sitting across from you at a desk, apparently deactivated and rendered in the game's typical crisp visuals. Ladies and gentlemen, Five Nights at Freddy's 6 has arrived.
During the ending with Cassette Man's Breaking Speech, you can see the building's temperature slowly appear in the bottom right corner... And it slowly ticks up to 100° and beyond as smoke and flames fill the screen.
The Lorekeeper ending gives you a picture of a quiet graveyard with six tombstones. Two of the tombstones are unreadable, but the others have the names Gabriel, Susie, Fritz, and Jeremy written on them.
If you were too busy trying to survive each night to pay close attention to the map, you'll receive one of these near the beginning of Cassette Man's final speech, when you look at the map and the pizzeria room in the center disappears, revealing that the vents that the animatronics were crawling around in were never connected to the pizzeria.

Five Nights at Freddy's: Security Breach

Just four words shown in bright neon on the true ending route: Freddy Fazbear's Pizza Place.
And if that wasn't enough, the player is entreated to an even greater one to follow — Springtrap being revived via a PizzaPlex Charging Station, hooked up in the very incinerator chamber he'd met his end in.
The ending cinematic of the true end reveals that a gigantic blob that might be Molten Freddy is making sure Springtrap doesn't leave the PizzaPlex.
In the 3-star ending route, in Princess Quest III, you'll find a locked room that resembles the one Glitchtrap traps the player in Five Nights At Freddys VR Help Wanted. Opening the lock frees Vanessa from Glitchtrap's influence.

Fazbear Frights

Epilogue 9 ends with Jake/Stitchwraith noticing that Renelle, the girl he saved, is wearing a heart-shaped pendant, which readers will recognize as belonging to Eleanor.