Family-Unfriendly Aesop: "Rumor Of Love" has one: if somebody's mean to you, humiliating them in front of the whole school is an appropriate reaction.
Foe Yay: Logan has this with all the females in the series, but its most obvious and biggest case is with both Dana and Zoey. Also with Lola, to a certain extent.
Fridge Logic: One episode the girls are trying to disprove the guys' theory that guys act different when hanging out with girls. So they disguise Lola as a guy. How does this prove their point if they don't know it's a girl?
"Funny Aneurysm" Moment: Zoey and Nicole fake-fighting in "Back to PCA" when you realize that Alexa Nikolas was fired because of real fights between her and Jamie Lynn.
Growing the Beard: Most people agree that Season 3 is the shows best season. Most people agree that the characters have the best chemistry in this season. While Zoey, Dana, and Nicole seem to have ok chemistry, Most people agree that Zoey, Quinn, and Lola have better chemistry. Added that all 6 of the characters (excluding Dustin) have a good friendship.
Harsher in Hindsight: Any episode dealing with the girls having an argument but making up at the end becomes this given Jamie Lynn Spears and Alexa Nikolas's dispute behind the scenes. Ditto for every friendship scene involving Zoey and Nicole, who were actually the closest of the girls in early seasons, they are harder to watch to watch due to the Hostility on the Set between the actresses.
Heartwarming Moments: At the end of "Lola Likes Chase", Lola senses that Chase isn't into her. When she talks to him about it, he admits that there's another girl. When asked who, Chase tells her that it's a girl from his hometown, and Lola lets him go. A later episode reveals that Lola was aware of Chase's crush on Zoey, but chose to spare their feelings.
In the season 1 finale, Zoey is helping Chase study for his biology exam by discussing dominant and recessive genes and the conversation briefly switches to what a theoretical child of Zoey and Chase would look like. The same episode also has Dustin asking Zoey where babies come from.
In the episode "Time Capsule," the teacher says that in 20 years people will be laughing at their clothes. Lola says that their clothes will always be cute - and although their clothes were in style back then, now they are completely out of style.
Lola's debut episode had her pretending to be a creepy Goth to stretch her acting skills. Victoria Justice's other well known Nickelodeon role was in Victorious were she played a character that went to a performing arts school and was friends/rivals with a goth.
Hollywood Homely: Quinn is a major example, as even with the stereotypical "nerd" indicators of glasses and funny haircuts she is noticeably very pretty, made more obvious during her make-over episode
Launcher of a Thousand Ships: All of the characters in the series (with the exception of Dustin) fall into this. Among the females Lola seems to fall into this and among the males Chase and Logan share this trait.
Rebecca's Laser-Guided Karma at the end of "Zoey's Balloon": the entire group tells embarrassing secrets to make Zoey's secret not look bad, then they all play the Macalana. Rebecca then flees in embarassment.
I had no idea #Zoey101 was this loved by so many people.
Moral Event Horizon: Coach Keller crosses this in "Wrestling" when he not only forces Zoey to join the wrestling team, but then admits that he was using her and that the whole reason he put her on the team was to get her in the tournament, make boys forfeit against her, and then lie to the ref saying she was "injured" so he could have another one of the wrestlers sub for her and get into the finals without being tired out.
Zoey is hated for being considered too perfect and being The Ace at everything she tries, barely having to work hard at managing two businesses over the course of the show so it's no surprise that she's on practically every sports team and is the object of every boy's affection (not to mention her somewhat hostile attitude that appeared out of nowhere around the second and third seasons).
James, the Replacement Scrappy for Chase. In the first episode he gets introduced he becomes part of the group, Zoey's love interest and every girl instantly falls in love with him.
Some Anvils Need to Be Dropped: The message of "New Roomies", that you and your roommates will have problems with each other, even if you're best friends, and you should try things out, is a great message especially for viewers going off to college
Logan and Quinn, an example that proves this trope does not make a couple bad. The two have little interaction for the first 3 and a half seasons, and the interaction they do have isn't friendly, without it being Belligerent Sexual Tension. But despite the relative lack of buildup and no real reason for them to get together outside of the writers' whims, the Opposites Attract chemistry worked and the pairing became one of the most popular on the show.
Zoey and James. He gets introduced in an episode and everyone instantly loves him, except Micheal and Logan, who still miss Chase. So in the end after everyone thought they were dating because they interacted, they end the episode with them getting together despite having no chemistry. Sort of Deconstructed as she later realizes she doesn't actually love him. It was still terribly executed and lead to the series' Seasonal Rot.
Zoey's Tekmate right beside the fountain receiving Chase's email saying 'I Love you' sent, but it falls down to the water as it vibrates, and short circuits.
The end of Goodbye Zoey when Chase admits it to Michael and Logan.
The final scene of 'Chase's Grandma', where Zoey comforts a sobbing Chase in the rain after his grandmother passes away.
In 'Michael Loves Lisa', it's hard not to feel bad for Michael when Lisa goes out with another guy.
They Wasted a Perfectly Good Plot: Given how Jamie Lynn Spears was on All That previously, and was shown to have good comedic timing, the writers could have used this opportunity to put Zoey in funny situations, and give her more of a Butt-Monkey. But no, they made Zoey too perfect.
Unintentionally Unsympathetic: Talking about what's above in the Designated Villain section, it can be very hard to be on Zoey and her friends' side when they actively mess with Logan to get him sent back to Anger Management. Their excuse for not wanting him to "weasel out of it" doesn't necessarily justify their actions in the episode. This is made even worse by Logan's supervisor still sending him back even though he's aware of what Zoey and the others did.
Zoey in "Dinner for Two Many". She wants a date with James without their friends, so they go to a fancy restaurant. Logan and Quinn are already there, along with Coco, yet the writers make it seem like they're at fault for ruining Zoey and James' date, along with Michael and Lola. The end shows them representing a private dinner, even apologizing for "ruining their date", despite Logan, Quinn, and Coco having no reason to feel bad. It's hard to feel bad for Zoey when all she does is whine the whole time in the restaurant, even getting mad at James for Michael and Lola barging in.
The Woobie: Stacey, without the slightest bit of doubt. In one episode she tried to audition for a play and got rejected before she could do anything. And in many others she and her cotton swabs are neglected. It should be noted in the show's final episode, Stacy doesget a happy ending. Granted she gets hit by a car, but the accident makes it possible for her to finally speak properly!.