Paige telling off two senior students that crashed Peter's party. She tells them You Leave Him Alone! when they grab Peter, and threatens to call the cops unless they leave. Peter is impressed and in the next strip apologizes to her for not wanting her and her friends around.
The first summer camp Story Arc may be the best writing Bill Amend's ever done. The first one, starting in June 1997 and ending in August, features a great deal of character development among Jason, Marcus and Eileen, and introduces Eugene and Phoebe Wu.
Three years later, the Wus and Eileen return for an epic six-week arc about who stole Eileen's camp journal, complete with a cliffhanger on every Saturday strip (meaning that those who read it in papers had to wait two days for the resolutions). Some highlights
Phoebe realizing that her brother Eugene had stolen the camp journal, just as her friends chased her away over a fight. She turns around, asks to borrow the detective hat, and tells Eugene he lost; she's forming a new friendship club where the friendship lasts forever.
The Earlier Story Arc about Peter and Denise's temporary break-up counts. Deep characterization and some heartbreak make for a great Tearjerker.
Any of Bill Amend's ego-stroking little insertions into his strip, like newspaper headlines about "Cartoonist marrying supermodel Paulina" ("'What a dreamboat!' says Paulina"), or "Cartoonist helps win World Series", etc. Also, the one time Andy was trying to convince her son Peter that rock stars are not the only babe-magnets "I hear lawyers 'attract 'em like nobody's business', too. And doctors. (And cartoonists)." Also, when Jason is trying to convince his mother that writing comics "is work. It is. ...Some of us just make it look easy."
Paige got two in the early days of the strip. One was where she punched a senior guy at his own party after he tried to get her to do bong hits, lines, and have sex with him. Another was when she kicked a sleazy guy at prom, after he grabbed her butt and later tried to "apologize" by asking her to "kiss it and make it better".
That latter arc is also awesome for Peter, who repeatedly warns Paige that the dude is a creep, approaches the guy before the dance to say in no uncertain terms that he will be looking out for his sister during the dance, and forces Paige to take along some pepper-spray in her purse (the threat of which finally makes the guy take Paige home).
Paige beating up Peter for insulting Morton; the fact that nobody else, Morton included, was even in ear-shot when Peter made his comment makes this double as a Heartwarming Moment.
Peter accidentally breaks one of Jason's toys, and Jason vows revenge sometime within the next 12 hours. Cue four strips of Peter running, hiding, and generally being paranoid. The last strip is the arc is Peter, scratched and bruised, pointing out that time is up, and saying that he rid in a garbage can, dove out of a second story window, and ate leaves and twigs for dinner, but Jason never(Peter's eyes get really big.)gothim. Jason: "Let's do this again, sometime."
Peter has, at multiple points in his life, reached speeds equal or greater than 1,000 miles per hour. In a station wagon.
Peter displays a surprising amount of maturity in an arc where Denise can't attend a winter dance with him, he can't get a refund on the limo he rented, and another girl named Mindy asks him out. After asking Denise if it would be okay, and finding out even the thought of him taking another girl would drive her to tears, he dithers for a weekend and tries flipping a coin even. Then he goes to Mindy and gently turns her down, explaining he's in a committed relationship and it would hurt Denise's feelings. He then introduces Mindy to his friend Steve who decides to interrupt the conversation. His bestie takes her instead, and Steve pays Peter for the limo. While it means Peter spends the night at home, with Jason, it was a victory for principles.