The ending, where Doctor Octopus was taking apart the reactor, staring up at it, and saying "I will not die a monster." Doesn't help that one of the next shots is the reactor floating to the bottom of the sea, Doc Ock drifting slowly with it.
The bit where Peter collapses after stopping the train. "He's just a kid! No older than my son!"
The passengers sticking up for him when Ock comes back. "You wanna get to him, you gotta go through me."
When Peter's glasses start to blur his vision again, considering what was motivating his powers to come back.
Jonah:It's All My Fault. I drove Spider-Man away. [...] He was a hero. I just couldn't see it...
Aunt May and Peter visiting Uncle Ben's grave and Aunt May saying "It wasn't fair for him to go like that. And it was all my doing." And later the scene where Peter tells her it was his fault that Uncle Ben died.
Earlier, Peter wakes Aunt May up from a nap, and before she raises her head and realizes what's going on, she asks Ben what he wants.
Peter daydreaming that he's talking to Uncle Ben, trapped in the memory of their conversation just before they go their separate ways prior to the wrestling match in the first film. When Peter tells Ben that he's retiring Spider-Man, Ben looks so defeated and heartbroken. You can tell he's not only crushed that he feels he's died for nothing, but he's sad for his surrogate son, too.