Many, many scenes with Amy. For example, when she makes her incredibly lame firearm joke and can barely contain her amusement. Also when Dave comes over to protect her and it's implied that John is actually setting them up on a date.
Amy is missing one of her hands, and goes on a long tangent to Dave about how everyone always treats her like a freak because of it, and always refers to her as "the girl with only one hand." Dave hadn't seen her in years, so he was surprised, but John saw her on a pretty regular basis, and talked to Dave about her pretty often.
Dave: Let me tell you everything you need to know about John. The reason I was surprised by your hand was because John never once described you as, "the girl with the missing hand."
As well as being downright hilarious, there's something very sweet about John questioning Monster Dave about his memory of his life, and then ending with a lame (and entirely in character for John) attempt to get 500 dollars out of him. This is going on when Replacement Dave is suicidal over the discovery that he is actually a creature from and alternate universe, so that line is the first sign that John is willing to accept Dave as Dave, even if he is the Tomato in the Mirror.
John has a toolshed filled with miscellaneous trophies and artifacts, most of them sent to him by lonely weirdos who think he's an expert on the paranormal. As John sarcastically says, "Everybody wants to help." Later in the story, Krissy Lovelace, a girl he and John had helped before, sends him her lucky gold cross in the mail, saying an angel had come to her in a dream and told her that he would need it. John repeats, "Everybody wants to help", sounding a lot more sincere this time.
After Dave has spilled his entire tragic backstory to Amy, she ends up telling him about why she was in Pine View. Eventually, we get this:
Dave: Antidepressants. The thought of [Amy] actually being depressed made me want to grab the whole planet and throw it into the sun.