The Daddy Long Legs item. When collected, the pop-up in the corner of the screen says 'Daddy's Love'. Daddy Long Legs' shadow follows you and his feet will stomp on nearby enemies. Even if that is not Isaac's actual father (per Word of God), the feeling of a boss labeled as a father trying to protect him warms the heart a little.
It becomes somewhat humorous when you fight the actual boss himself with the item collected.
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.
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, as if to say that even in the darkest pits of his life, the divine still want to help him find his way to safety. And unlike the shops or Deals with the Devil, these items have no strings attached aside from only being allowed to take one.
This turns out to be Foreshadowing. In the final ending, despite Isaac's belief he was cursed or evil, God directly intervenes to help him by throwing a lightning bolt which destroys the Beast. Afterwards, Isaac flies up to Heaven and is reunited with Guppy.
The Brother Bobby and Sister Maggy (likely Isaac's dead siblings) items as well as Cricket's Head and the Guppy items (Isaac's dead pets) items. It may not be much, but the thought 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.
On the birthday of Satoru Iwata, the daily run of Afterbirth has Isaac changed into a skin of Iwata.
At least one picture of promotional art has Isaac bawling uncontrollably and wetting himself in the presence of several of the game's first bosses (Gemini, Monstro, Duke of Flies, Pin, a Gurgling, Fistula, Peep, and Larry Jr.). Thing is, they aren't being menacing at all and actually look a little worried and concerned. Even if this never happens in-game (unless the usable items like Monstro's Tooth count as real Heel–Face Turn scenarios), it's kind of touching to see these monsters not torment Isaac for once.
The final ending of The Legend of Bum-bo ends on a really bittersweet note where the narrator transitions fromhis raspy Bumbo voiceinto his normal one, as Isaac's father tells his son that even though he is leaving the family, the world they created together will always be there when life gets rough, and he will always be with Isaac in spirit. Even with how much of a Crapsack World the basement seemed to be in the game proper, it was Isaac's world that he created, and in his Dying Dream he goes through it just to play with his dad one last time. As Heartwarming in Hindsight as it is depressing.
The Narrator/Isaac's Father: This world of Bumbo's will grow and grow, and always be there for you as a way to escape from the real world. There is no end to your imagination, no limit to what you can create. When things get difficult, you can go there. When you feel weak, you can escape into this world we created and become powerful. Always remember this, Isaac: your imagination knows no bounds, and I'll always be here waiting for you. In our next adventure together.
Isaac's Father: Ok, so: "Bumbo lived in a box, behind a hill. Bumbo had his trash, his coin-" Isaac: No, Daddy - do it in the voice! Isaac's Father: ...you want me to do the Bumbo voice? Isaac:Yesss! Isaac's Father: You got it. (ahem) (screen re-transitions into the actual intro) Isaac's Father/Bumbo:"Bumbo live in a box behind house on hill..." [...]
Doubling as Awesome, one of the bosses from Antibirth, Baby Plum, returns in Repentance. Your first instinct will be to immediately start attacking, because, you know, boss fight, but on the off chance you decide NOT to fight her and instead wait it out, eventually she'll wave bye bye and leave... and the boss fight concludes with her leaving an item called "Plum Flute". When activated, it summons Baby Plum to fight for you, and given how she likes to bounce around the screen and spray bullets all over the place, it's very useful. In a sense, your pacifism turns what would be justified self-defense into a charming (albeit still dangerous) game of play fighting. The Plum Flute's description is even written as "Play time!"
The Beast ending in Repentance encapsulates entirely the themes of the game until this point. Isaac's father recities the tale of his leaving, his abusive nature, his mothers descent into madness, Isaac's soul crushing guilt at all of it, the grief of Isaac's mother discovering his remains in his toy box, and it all culminates into Isaac's ascension to heaven and reuniting with Guppy as he views his mother and father at the moment of his birth when they were happy together. It looks like Isaac is finally ready to accept what's happened... and then Isaac's father stops telling the story and talks with him a bit, reminding him that he's the one telling the story and asking if he really wants it to end like this. The game hasn't been Isaac's dying dream after all, but a bedtime story told by his father with his son's help. All of this is driven home by switching one word for two in an otherwise book ends conclusion to the game that makes it clear that the new story they're telling isn't just another loop of a supposedly dying Isaac's imagination.
Isaac's Father: Are you sure this is how you want this story to end, Isaac? You're the one writing it, it doesn't have to end this way. Here, how about we tell it a different way? Maybe a happy ending? Isaac: Okay, Daddy. Isaac's Father: Good. Are you getting sleepy yet? Isaac: Yeah. Isaac's Father: Okay, so... (ahem) "Isaac and his parents lived in a small house on the top of a hill..."
The ending of the game is left purposefully ambiguous (with Edmund stating that it's certainly not as simple as it seems), but it's clear that the pain Isaac felt during his life is over. A more bittersweet interpretation is that defeating Dogma and The Beast represents Isaac finally understanding that he was never at fault for any of it. He still dies, but his self-hatred, traumas and perceived sins are left behind (represented by ??? and the Forgotten) as he ascends to heaven. What happens after he dies is anyone's guess... maybe he received another chance at life, maybe he imagined it just before his death. Maybe simply telling bedtime stories with his father is his personal heaven.
The implications of the Dogma boss... and item. He defeats the representation of the twisted Christianity taught by extremist televangelists... but still chooses to take up the cross, the pure and good dregs found at the root of Christianity. He has discarded the bad but held on to the good, staying true to his beliefs and using the power of God to defeat the root of his sin and find his own peace.
.Isaac's Father: Ok, so: "Bumbo lived in a box, behind a hill. Bumbo had his trash, his coin-"