Season 2's "Road to Damascus" had Ben and Sophie give into their passions while in a 1930s truck cab/car. When Sophie finishes, a massive rainstorm begins. Ben sticks his hand outside the cab/car window to catch the rain, then gently puts it to Sophie's cheek. Subverted when Sophie leaves the Carnivale at the end of the episode. Subverted even more in the final episode by Sophie's Face Heel Turn.
The moment in "Pick a Number" when Lila and Ruthie dress Dora Mae's dead body in a bolt of silk they'd been saving, telling her stories while they clean her up.
This troper's got to give it to "Lincoln Highway", where Ben tells Libby to trust him and run as far from the tarred, feathered, and dying Jonesy as she can get. She does, crying her eyes out because she thinks her husband is going to die without her there, and Ben uses the life from the vultures that have gathered around Jonesy's almost-corpse to bring him back to life. Jonesy gets up, takes a few steps, then lets out a whoop of joy - Ben hasn't just healed him, he's healed his crippled leg, too. Jonesy's pure and unadulterated joy is just amazing.
This troper couldn't stand Rita Sue for most of the series, but the moment in "New Canaan, CA", where she stands at Ben's side against the other carnies, sticking up for him when she'd previously been one of his main critics.
Another subtle Rita Sue moment is her terrified search for Libby after Dora Mae has been killed and Libby is missing. Libby shows up, smoking a cigarette and insulting her mother for worrying, and Rita Sue first slaps her across the face, then hugs her tight, crying.
The ending of the season two finale when the carnies find Ben lying unconscious in the cornfield, Samson shouts "He's alive!" and they lift him up and carry him back to safety, thus cementing the fact that he is one of them.