Stanley and his coworkers are being constantly secretly monitored by their employers via cameras. There is also a rare instance where the Narrator claims that Stanley is being followed upon leaving his office at the beginning of a new run.
In a easy-to-miss corner of the Memory Zone, there is a small rock with "In Loving Memory: Little Stanley" engraved on it, along with a small photo of a presumably deceased pet.
Stanley's head, along with his entire body, is violently crushed in the Museum ending. This isn't shown on screen, only being described and later heard.
In the Explosion ending, the Narrator tortures Stanley by trapping him in a dangerous situation and watching him struggle to escape. Meanwhile, in the Zending Stanley tortures the Narrator by repeatedly hurting himself to ruin the Narrator's happy ending, or by trapping him in eternal solitude in the Skip Button ending.
One of the prompts in the apartment ending is to read your kids a story, implying that Stanley is a father. Stanley dies in several endings. Given that the Narrator says that Stanley's wife isn't real, however, it's debatable that the kids are real either.
There is an obscure easter egg where a clown mask from the game Payday can be found on the ground during the Confusion ending, though this can be easily missed.
Not in the traditional sense, but in the Not Stanley Ending, the Narrator separates the player from Stanley, forcing the player to watch Stanley from above, unable to control him. This implies that Stanley was being “possessed” by the player and forced to harm himself in various ways to obtain all the endings. However, Stanley is unable to move without the player, perhaps implying that he doesn’t have any sort of free will.
In more than one ending. The Insane Ending involves Stanley beginning to believe that he isn’t real and having a crisis, and the Not Stanley Ending involves the Narrator separating the player from Stanley.
Stanley and his co-workers are watched in an underground facility. In addition, it's possible to see someone watching Stanley in the background of the No Buckets and Bucket Elevator endings.
The Mariella ending involves Stanley going "insane" and dying. Upon discovering his corpse, Mariella's first thought is to be grateful that she's more "normal" than he is.
The game has multiple endings; some are happy, some are sad, some are in-between. Endings are never really final, as restarting and looping through the game to get different endings is kinda the whole point of the game.