Given what absolute pricks both you and Alexander turn out to be, "heartwarming" is a somewhat subjective concept in this game. Still, one could argue that the "standard" ending in which Daniel destroys Alexander's portal and declares his victims avenged is more heartwarming than the "good" ending in which he is allowed to gain some form of cosmic existence he arguably didn't deserve.
When, in the bad ending, Alexander says that he can finally go home. Also, the way Alexander thanks Daniel and tells him he'll be celebrated forever.
Agrippa: "Don't worry, Daniel. It will be all right."
While it doubles as a Tear Jerker and horror, the mother allowing her daughter to escape, not caring about her own safety. And later on, while she's sobbing her eyes out, refuses to tell Daniel where her daughter went.
In an odd, creepy way, the fact that Alexander was willing to murder and torturehundreds of people, manipulate people, and almost get arrested just so he could see his wife and family again is kind of heartwarming.
The Back Hall. After escaping the nerve-wracking Cellar Archives, you're in a peaceful place with soothing music playing in the background.
In the custom story The Great Work, by the end of the penultimate chapter, the protagonist is free from the object that caused him all his problems; he could just walk away and live a normal life, but he decides to go back and save his ally. Also, the two best endings:
He retrieves the Orb and flees. He hasn't been able to save Samuel, so he decides to further his legacy: he creates another immortality potion and drinks it, so that he can continue to protect the Orb in Samuel's place.
He retrieves the Orb and, risking his life, finds Samuel in the prison and gives the Orb to him. Samuel opens a portal and the protagonists jumps in. He awakens and finds a final letter by Samuel, along with a parting gift: an amnesia potion that will make him able to return to a normal life without being haunted by the horrors he witnessed.