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 boss - who is very intimidated by her - 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.
Sheldon finally admits he loves Amy in "The Prom Equivalency".
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.
Cute but Cacophonic: Apparently when Bernadette gets excited, her voice gets so high pitched animals get annoyed.
Gigantic Gulp: Amy and Bernadette drink margaritas from huge glasses in "The Focus Attenuation".
Heel Realization: Bernadette thought she was a sweetheart, but it turns out most of her friends and co-workers are intimidated by her and sometimes offended by her remarks. Learning about this she is brought to tears, not realizing she came across like that.
High School Dance: The gang organize a private prom in the roof of their building as a redo for their own missed proms.
Hopeless Suitor: Deconstructed with Dr. Lorvis (played by Billy Bob Thornton), who in "The Misinterpretation Agitation" tries to woo Penny after confusing her sales tactics for affection and later does the same with Amy.
Hypocritical Humor: Howard making jokes about Dr. Lorvis still living with his mother. Raj is not amused.
In Memoriam: The ninth episode in the series, The Septum Deviation, incorporates homage to Carol-Ann Susi (Debbie Wolowitz) who sadly died during the screening of the new season. See here.
The "I Love You" Stigma: Defied. Amy was working up the nerve to tell Sheldon she loved him and prefaced it with a long-winded ramble about how she isn't expecting anything in return. Sheldon ended up cutting her off by saying "I love you too," explaining he already concluded love was the only explanation for his feelings for her.
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.
In "The Misinformation Agitation", Dr. Lorvis locks the guys in his rec room while he tries to go out with Penny. Only they don't mind since they're too busy playing Donkey Kong.
Love Confession: In "The Prom Equivalency", Amy tries to make her feelings for Sheldon known but Sheldon beats her to the punch.
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.
Pass the Popcorn: While Leonard confronts Dr. Lorvis about trying to date Penny in "The Misinterpretation Agitation", Sheldon, Howard and Rajesh stand by the doorway, Chinese take out in hand.
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.
Stalker with a Crush: Dr. Lorvis. He's shown to be a very shallow person who doggedly stalks any women who makes physical contact with him. Indeed, the girls find him extremely creepy, and when they learn he's locked the boys in his game room the girls forcefully march him back to free the boys.
Amy: Sheldon, there's something else I've been wanting to say. But before I do, just... I want you to know you don't have to say it back. I know you're not ready, and I don't want you to say it because social convention dictates... Sheldon:I love you too.
Wiki Walk: In "The Focus Attenuation", the boys try to come up with new inventions, but keep getting sidetracked watching movies and looking up random stuff on the internet.