Bait and Switch: While stuck in a car, Sheldon asks Amy to plug her ears so he can talk to Leonard in private. He then tells Leonard he's interested in a sexual relationship with Amy. A few beats later, he reveals it as a ploy to see if Amy really can't hear them, and then moves on with his true intentions.
Beware the Nice Ones: While always a part of her character, apparently Bernadette intimidates most of her co-workers, intentionally or not. Penny gets a job as a pharmaceutical rep by bonding with her co-worker over this.
Character Development: Penny is slowly becoming more responsible with her own life by accepting her acting career was a bust. While not really thrilled with being a pharmaceutical rep, she recognizes the need to step up and do her homework for once.
Clark Kenting: Discussed on "The Expedition Approximation" when Raj explains Hannah Montana to Sheldon, and Sheldon finds it absurd that she could pass unrecognized just by wearing a wig.
Raj: But you're okay with Superman concealing his identity with a pair of glasses? Sheldon: He doesn't just put on a pair of glasses. He combs back his curlicue and affects a mild-mannered personality.
Gigantic Gulp: Amy and Bernadette drink margaritas from huge glasses in "The Focus Attenuation".
Important Haircut: Penny sports a shorter pixie haircut as part of a new adult look. Sheldon, of course, hates it.
Jerkass Has a Point: One of the astronauts who bullied Howard in the ISS told him not to take the first pitch on the Angels game. If he succeeds, nobody cares; if he fails, everyone laughs at him. Howard fails.
Locked in a Room: Sheldon and Raj spend much of "The Expedition Approximation" down on a steam tunnel under the university to practice for when they have to do dark matter experiments on an abandoned mine.
Mistaken for Pedophile: Invoked when Howard, Raj and Sheldon suggest a way to bring more customers to Stuart's comic book store.
Parental Favoritism: When Stuart moves in with Mrs. Wolowitz, Howard becomes jealous that she treats him better than her own son.
Personality Swap: When the girls go to Vegas in "The Focus Attenuation", party girl Penny has to stay and study, while the usually more responsible Amy and Bernadette go get drunk.
Plot-Mandated Friendship Failure: A rather subdued example, Penny and Bernadette clash over how casually Penny was treating her new job. Most of the plot was how Amy was stuck as friends to both and was happy over the new focus on her. Penny and Bernadette civilly talk things out, which left Amy a little disappointed.
Discussed on "The Hook-up Reverberation", when Sheldon mentions research suggesting that a man entering a romantic relationship loses an average of two friends as a result, in regards to Rajesh and Emily's relationship.