Just about all of the interactions between Peter and the Cutie Mark Crusaders would qualify for this, particularly their first meeting, when Peter gets inducted as their captain while he wasn't paying attention to them.
Some of Peter's classical witty banter while fighting.
Fluttershy's uncalled arousal.
“Hold your tongue, knave!” Luna shot back, slamming her hoof into the ground. That same instance, lightning erupted from the sky, directly overhead the irate mare. “I am no bat!”
Peter remained still but allowed a nervous chuckle to escape from his chest. “Noted. You're reminding me more of Thor now.”
Velvet's question to Peter and Twilight in chapter 35.
Lyra's mishaps while trying to prove Peter's identity as a human.
Peter meets Babs Seed. His response? "Oh God! They're multiplying!"
It took over forty chapters, but a 60's Spider-Meme finally found it's way in. When a now human Twilight comments on having 'tentacles at the ends of her hooves,' Peter says. "I've seen enough hentai to know where this is OW!" (His remark earned him a smack upside the head.)
Peter brings a bunch of gems to Tony Stark to get some money. Tony, being who he is, sets up a bank account with three hundred million dollars. Peter faints from the sheer amount. Again, being who he is...
Called back in Chapter 60 when Peter ends up giving the diner he and Twilight frequented to its manager as well as a hefty tip, implied to be several million dollars. As she passes out, Peter said, "So that's what it looked like."
This gem from Spidey and Twilight's first encounter.
Twilight glanced to the side, retreating into the confines of her mind for any recollection regarding the given location. After several moments, her eyes sprung open at a late realization. "Earth? Human? I've never heard of anything like those. The fact that you're bipedal is unusual, but..." Closing her eyes, Twilight frowned. "You are not physically and scientifically possible."
'The talking horse is telling me I don't exist? I don't know whether I should be terrified or insulted.'
Early on, Spidey is a bit embarrassed of Twilight helping him practicing shooting webbing for his horn, because, "Don't you think it's a little unusual for a girl to watch a boy shoot a sticky, white substance out of his horn?". Of course, Twilight doesn't get it.
During the race between Spider Mane and Spitfire, Trixie getting roped by Pinkie Pie into cheerleading
Trixie sighed. Only today would she stoop so low. “Hoo-rah. Hoo-rah.” The unicorn blankly stated, mirroring Pinkie Pie’s motions with an immense look of exasperation. “Spider-Mane. Hoo-rah.”
Peter meeting Twilight's parents for the first time.
'Fighting super-powered crazies is much easier than this. Is that even natural?'
Not that Twilight escapes unscated...
Twilight Velvet: "You're handsome, too. It's nice to see my daughter has lovely taste."
In the middle of the battle with Sombra, Spidey strikes again.
“Okay, I have a confession to make,” Peter murmured, attempting to ignore the throbs coursing through his cranium. His spider sense was only reacting to the heightened level of danger that was brewing above.
Shining glared at the mist cloud, scoffing harshly once it took the form of a tornado. “I know. Sombra destroyed my crystal heart, too.”
Spider-Mane shook his head. “No, not that. It's worse.”
“I think I'm pregnant,” Spider-Mane suggested inanely, earning a baffled expression from Shining Armor. After an awkward silence occurred between the pair, Peter raised his hoof and nodded. “Oh, and Twilight's the father.”
Fridge-induced: spreading wings was previously established as a sign of Pegasus' arousal, and when Twilight, now an Alicorn, hugs Peter at the end of chapter 30 she suddenly spread wings.
Spike: "Your aunt’s awesome, Peter, but why does she keep calling me Barney?"
Peter: "You don’t want to know. I still have nightmares from my childhood about that guy."
Twilight's comment when she drags Peter at a Victoria Secret store and lets him unable to speak when she shows off to him:
"Speechless. I’ll have to tell Trixie about this."
Meta: Twilight replaces MJ, according to Word of God. Hilariously, Tara Strong voices MJ in Ultimate Spider-Man.