Heel Realization: Bernadette surprised herself when she realized she was wrong to try to keep Howard from taking his chance at realizing his dream.
Daydream Surprise: The entirety of "The Recombination Hypothesis" was a daydream by Leonard trying to figure out his feelings for Penny and their future. The relationship fails, but he still decides to ask her out again in real life.
Long List: The list of things that were stolen from Sheldon and Leonard's apartment, most of which were video games.
Mildly Military: Sheldon gives himself the Paintball rank of Captain, citing Kirk, Crunch and Kangaroo as examples. He sews Army Captain's bars to his uniform, but the three he references are Navy/Coast Guard Captains, the equivalent of Army Colonels.
Mutual Disadvantage: To decides who gets Prof. Rothman's office, Sheldon and Barry play a one-on-one game of basketball, under the notion that they are equally bad at sports, putting them on an even field. It works too well, in fact, as neither manages to score once after 45 minutes.
My Friends... and Zoidberg: Sheldon refers to the rest of the group as his "three friends and one treasured acquaintance", who turns out to be Howard.
Milestone Celebration: The 100th episode, "The Recombination Hypothesis", in which Leonard decides he wants to get back together with Penny.
Paintball Episode: After Sheldon's Death Seeker action in being a horrible leader, he ended up inspiring the guys to take back the game and the won the inter-department paintball game for the first time.
Relationship Upgrade: It was a real shock when Sheldon asked Amy to make their relationship official.
Unwanted Gift Plot: Amy gives Penny a tacky painting of the two of them, insisting that it be displayed prominently in her living room. It is supposed to be hung on the fourth wall, which is why it hasn't been seen since.