The story is a parody of Peggy Sues in which Harry quickly lampshades everything weird about the story and has a blast doing it. Of course it's going to have more Funny moments than can be listed.
Any time Harry brings up his " psychic" scar.
In a similar vein, the rumor Harry started up that Draco is the love-child of Narcissa and Snape. This, more than anything, becomes the cornerstone of their new-timeline relationship for years to come.
Chapter 15 is full of these moments. For instance Luna trying to convince Hermione to subscribe to the Quibbler when Harry walks in on them.
"I wouldn't bother with her just yet, Luna," Harry told her. "She's just not ready."
Immediately, Luna's expression became much more somber. "I am so sorry," she said sincerely.
"What do you mean you're sorry? For what? And what am I not ready for?" Hermione demanded, looking a bit affronted.
Earlier in said chapter it's mentioned that due to the writing of the Chamber of Secrets everyone has been trying to check out the two copies of Hogwarts a History. Hermione questions how Luna knew she didn't believe in the Great Pumpkin and Luna says she overheard her talking about it in the Library.
"What were you doing in the library?" Hermione asked, uncertain she wanted to know.
"Checking out two copies of Hogwarts: A History," Luna replied brightly.
Harry laughed. "I love you Luna, I really do."
Sirius as a teacher. Also, his plan for dealing with Snape: Leave him alone until the paranoia builds, then start pranking him. Which he does. By changing his appearance on a regular basis.
Sirius and Harry teasing Remus about Tonks' attraction to him. When Remus, confused, asks if Sirius is going to threaten him about breaking her heart, Sirius merely says that she's going through Auror training, then adds this gem.
And I'm sure she could castrate you far better than I ever could.
In chapter 17, Lee Jordan and McGonagall do commentary at a Quidditch game.
McGonagall: Jordan. Do try and pretend to be impartial.
Jordan: But Professor, I didn't even insult those dirty, rotten-
Harry: So what are we going to do this summer, Sirius? Sirius: The same thing we do every summer, Harry. Harry: Try to take over the world? Remus: Yeah, that settles it: you two are not allowed to be left alone together.
When Neville confronts a boggart, it takes on the form of Harry as Minister of Magic.
Boggart Harry: You know, Monday is probably the most depressing day ever, let's cancel it. And what's this nonsense about not being able to own a dragon in Britain? I say we give one to anyone with a license. Oh! And we can add a dragon tax to the Pureblood tax! And how did the ghost community respond to my decree to allow Sir Nicholas into the Headless Hunt?
And Harry's Reaction to all this? He'd never thought of being Minister before and now wants to run for Minister of Magic and thanks Neville for the idea.
When Hermione asks why Harry is deliberately trying to lose the House Cup, he explains:
Harry: I believe that the House Cup is a school-wide conspiracy to try and spawn as many teacher's pets as they can and encourage teacher's pet-like behavior in everyone. Snape and I are doing all we can, but we can't lose Gryffindor the House Cup alone!
Hermione: You have problems.
Chapter Fourteen. All of it.
Harry, upon meeting Cedric for the first time, advises him that if he is ever suddenly transported via portkey to a graveyard, to grab the portkey again and/ or run like hell. When the "fourth book" timeline really kicks into gear, every time Harry sees or speaks to Cedric, he prompts him. Soon, the conversations go like this:
Cedric: (without batting an eye or thinking) "Run like Hell."
Hilariously, this backfires when Cedric is portkeyed to the graveyard and has a minor panic attack.
Harry becoming the champion of Salem Witches' Academy for the Pentawizard Playoffs, while "Fred Weasley" becoming the champion of Harry Potter School of Awesomeness (its headmaster being none other than Gilderoy Lockhart).
Chapter 24. Especially this gem: "I'll give you the mass murderer thing," Harry said. "But the whole effect is ruined by the fact that you keep a Diary. I mean, honestly, what's with that? It's like 'Dear Diary, today I went and slaughtered an entire village of Muggles. Aren't I diabolical? And no, I am in no way compensating for the fact that my father abandoned my mother before I was born. And no, said father was not a Muggle, where are these dreadful accusations coming from? They are distinctly not fabulous.''
In chapter 45, when Ginny volunteers to be the thing Harry needs to get in the second task. He gives her his "favorite lucky rock" which is actually a time-activated portkey. Harry's plan is to not have to go into the lake at all.
Ginny: You don't have to do this..
Harry: I know, but I want to. Besides, this way you know at the very least I'll be trying to get my rock back.
Dobby gets this hilarious moment:
Harry: Wait... Didn't Draco order you not to try to save my life or to try and drive me from the castle?