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All Girls Want Bad Boys: Slightly inverted in that Macy wants a Jonas regardless of who or what he does, and also in that Stella obviously wants Joe (the closest thing to a 'bad boy' of the three - but they've known each other since they were babies, and Joe would never act like that around or to Stella.
Book Ends: The beginning of season two opens with the band singing "L.A. Baby", and the final scene is them playing it again, acoustic this time.
Bottle Episode: The Tale Of The Haunted Firehouse. All of it was filmed inside the firehouse, effects and props were limited to a few skeletons, a handful of tech equipment, and lighting. And not only that, but the majority of it was filmed on the camera Kevin has. Behind the scenes photos showed that it was them holding the handheld camera.
Brother-Sister Incest: Or, well, brother/crossdressing brother incest, and averted, because Nick shoots Kevin's idea of dressing Nick in a wig and a dress to be Joe's "mystery girl". (See Wholesome Crossdresser below.)
Butt Monkey: The boys all get it in one way or another, but Kevin gets it the most.
Nick: Brothers don't let brothers make fools of themselves. Kevin, I'm sorry I've let you down for so many years.
Cloud Cuckoo Lander: Kevin. Macy has her moments too - but as of Jonas L.A., her head is on straight.
Continuity Nod: Two of the games Macy has out to play with Frankie in Jonas L.A. are Word Hole and Dopey Doctor, both of which were played in the first season.
Cursed with Awesome: Also another drawing points of the show (as it is with Hannah Montana, where being a world-famous singing group just sometimes doesn't mesh well with normal life. Four words: 'Taking out the trash'.
Cut Short: Lasted for only two seasons and 34 episodes, tied with Cory in the House for shortest-run Disney Channel Original Series (until So Random! was cancelled in 2012, after only one 26-episode season).
Coler: Don't you think you're being a little full of yourself?
And "Home Not Alone"
Macy: I almost choked on a Kevin head and nobody even noticed.
"Karaoke Surpise" after Stella catches Macy and Joe together.
Joe: We're doing mental math. It's like jumping jacks for the brain.
Stella: Well I just came to drop off these pants to go with the shirts. And now I'll go. Don't want to keep you two from adding your figures together.
"Direct to Video" opens with a scene of the boys after a crazy night. It is very obviously a metaphor for a hangover.
Joe: After the fourth slice of pizza it's all just a blur.
The full version of the theme song has the line "I drove her home and then she whispered in my ear 'the party doesn't have to end, we can dance here'", which sounds an awful lot like an invitation for sex.
Obfuscating Stupidity: In season 2, when Macy realizes that Nick and Kevin don't remember she plays sports and plays them well, she does this to hustle them.
Once an Episode: They sing or play a song at least once an episode, and it's lampshaded in one episode where Kevin takes or picks up a guitar and the lights turn out, and Joe or Nick leans over and says "turn on the lights and put down the guitar, we don't have time for a song".
She's Not My Girlfriend: Joe gets detention to prove to his friend that he really is a normal guy who doesn't take advantage of being a rock star. Everyone just assumes she's a Girl of the Week which is why he's doing this leading to the trope. It's a subversion in that Joe does this to a guest character who he genuinely isn't interested in.
Shorter Means Smarter: The shorter/younger the brother, the smarter. From Kevin being a Cloud Cuckoo Lander and Joe being so self-confident he's prone to stupidity to Nick being the most sensible brother and Frankie being incredibly cunning.
Shout-Out: A whole sub-plot of an episode makes fun of the whole CSI: Miami meme of "witty comment, glasses, YEEEEAAAAAAAHHHHHHH!!" as well as the CSI camera angles.
Joe's movie Forever April is basically Twilight but with a supernatural ghost girl rather than a vampire.
To Corey Hart in season one: "Let's not be those guys who wear their sunglasses at night."
Shown Their Work: One Running Gag in season one was Macy always having sports equipment, and even though it rarely got anything more than a quick gag about her nearly killing one of the guys, the equipment she has is always accurate and appropriate for whatever sport she was doing at the time.
Sorkin Relationship Moment: Inverted; in 'Karaoke Surprise', Stella shows up at the guys' place to confront Joe and Macy - and then, finds out mot only that they've planned a 'fifteen-year friend-iversary party' for Stella, but that Macy would never do that to her, because she (Macy) has already realized that Joe and Stella have feelings for each other.
Wholesome Crossdresser: Averted. In "Frantic Romantic", when they say they need a mystery girl for Joe to get rid of Fiona Skye, Kevin immediately suggests that they put Nick in a wig and a dress. (Nick shoots him down.)
Wish Fulfillment: Stella and Macy for the female audience. Stella is a beautiful, fashionable girl who is childhood friends with the brothers and grows up to be a Victorious Childhood Friend to Joe. Macy is an Asian-American Demi Lovato looking Expy who is great at every sport and, despite her clumsiness around the boys, quickly becomes an Ascended Fanboy and is now one of their close friends plus Nick's new Love Interest. It's like the writers read Mary Sue fanfiction.
In the case of Macy/Nick, that's one part Character Development in action (for Macy), and one part What You Are in the Dark (for Nick). Once she got to know them as actual people instead of just stars, she could relate to them a lot better, and vice versa. That's why it was Nick who started chasing after Macy, and Macy who was about to walk away and not look back when Nick momentarily Took a Level in Jerkass.