The implications of certain items, alongside their interactions with characters in the game, can create these.
The Egg Sack item. When collected, the pop-up in the corner of the screen says 'Daddy's Love'. What does it do? It means that Daddy Long Legs' shadow follows you and his feet will stomp on nearby enemies. Remembering that Isaac's own mother is out to get him, the idea of his father trying to protect him warms this troper's heart a little.
Mitigated a bit though by Word of God who stated that Daddy Long Legs in not Isaac's father. Still nice that a boss would help you though.
A bittersweet moment, given what happens during the main game, but in the 13th Ending and The Polaroid, we see Isaac's Mother cheerful and accepting of him.
YMMV, but in version 1.4 of Wrath of the Lamb, we finally have a not-chance-based way to obtain the Polaroid. Mom is keeping it.
God, or at least an Angel can appear and offer Isaac an item himself.
The Brother Bobby and Sister Maggy (likely Isaac's dead siblings) items as well as the Max's Head and Guppy's paw (Isaac's dead pets) items. It may not be much, but the though of Isaac's loved ones still being able to help him even in death goes a long way to show that he isn't truly alone.