- The Christmas episode. Specifically, the scene where Brain reads Pinky's letter.
''"Dear Santa, hello, hah hah, narf! This year Santa, I ask for nothing, but I wish to tell you about my dear friend, the Brain. He is honest and very hard working, and only wants what's best for the world, but he gets no reward. He is only greeted with defeat. He never gives up, but I know it must be very hard, so please, take anything that you have for me and give it to my best friend in the whole world, the Brain. Love Pinky. (PS. By any chance do you have in that big old bag of yours the world?)"
- The Halloween episode.
- A more minor example, the ending to "The Brain's Apprentice". Brain's robot uprising was very close to succeeding but due to not listening to Pinky and not paying close enough attention, the plan stalled and backfired. When Brain finds out what happened, he stares at the screen sadly as the score gets mellow. Slightly averted in that it's also played for laughs.
- "This Old Mouse"
- Brain's downward spiral into depression after viewing a possible future where none of his plans ever succeed. He practically gives up on himself, getting rid of all of his belongings and moping around the lab.
- Brain temporarily moving out of the lab, leaving Pinky alone.
- And of course, Brain's death in an avalanche. Even though it's avoided by the end of the episode, seeing it unfold (especially from Pinky's perspective) can be a little devastating.
- Really, a lot of of Brain's abuse towards Pinky in earlier episodes can come across as a little cringe-worthy, like in the first episode when Brain grabs Pinky's ear and yanks on it forcefully, all while Pinky is clearly in pain. Their relationship became slightly less antagonistic as the show progressed, however.
- Billie and Brain's backstory in "Brain Noir". Brain became too absorbed in world domination to carry out a relationship with Billie.
Trudy: You're in love with her aren't you?Brain: With who?Trudy: THE WORLD!Brain: Yes....
- Something similar happens with Brain and another female mouse, Trudy, in "The Third Mouse".
- In "The Family That Poits Together, Narfs Together," we see Pinky watching a soap opera featuring a family reunion. He becomes increasingly emotional about it, and breaks down in tears, having not seen his family in several years, obviously missing them dearly. (Which makes it all the more sweet when he does eventually reunite with his parents later in the episode.)
- The ending of "Brain Acres" where Pinky and Brain have to bury Maurice, an anthropomorphic carrot Pinky becomes attached to. Pinky sings a sad song as they bury him and he finally starts crying.
- The song in question is a spoof of "Born Free", and surprisingly enough, it works.
- The ending to "Two Mice and a Baby". "Bye bye....Dada."
- Brain's flashback and Freudian Excuse from "Leggo My Ego".
- Mr. Sultana's life and backstory in "My Feldmans, My Friends".
- The ending to "Pinky's Plan", which also doubles as heartwarming.
Brain: I don't deserve a friend like you Pinky.
- In "The World Can Wait", Brain finally finds love with a neighbor lab mouse, however just as he's finally won her over, she gets experimented on, leaving her traumatized and with a bigger IQ than his own, pressuring him to call off the romance until he has taken over the world before she does.