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Near the beginning of "Where No Mouse Has Gone Before" — the duo's distorted faces when the mini-centrifuge they're on reached high speeds can haunt anyone's dreams.
The giant, living vegetables in "Brain Acres." Brrr.
The scence from the jungle episode where the carcass of a warthog was shown.
From "Opportunity Knox": "TURN OFF THE RADIO, PINKY!!!"
Nevermind the few times Pinky has gotten much further than Brain in taking over the world, even becoming President of the United States once. And in contrast, many of Brain's evil schemes run on Insane Troll Logic, and even while some of them can be excused since they live in a crazed cartoon universe, they way he goes about achieving them is often stupid enough that Failure Is the Only Option anyway.
Word of God has confirmed that the theme song leaves it open to the readers to decide...
Creator's Pet: Elmyra. It's slightly different, though, because even the writers hate her- it's the executives that love her so much.
Also 'Two Mice And A Baby', in which P&B's plans to use an extraordinary child who literally falls into their hands are put aside when they realize a Human couple will raise him better. The baby waves a tender goodbye to Brain and calls him 'Dada' causing Brain to tear up. Of course the audience realizes all along that the baby is Kal-El.
The mice made cameos in the two prime-time Tiny Toons specials, and both cameos had them in scenes prominently featuring Elmyra. Apparently, this must've been where they got the idea for the aforementioned Retool.
Snowball's last appearance, "Brainwashed Part 3", aired right around the time his voice actor died.
The episode where Pinky and the Brain create a paper-mache replica of the earth, so that they can convince everyone to relocate and they can take over the real world. The background music during the montage of them building the thing? Dvorak's Symphony no 9 "From the New World."
Much like parent show Animaniacs, P&TB frequently took quite a few jabs at Disney, yet ended up as one of the last shows added to the Toon Disney lineup. It was last seen working the late shift on weekends during the first few months of the existence of successor Disney XD.
One episode, a Winnie the Pooh parody, has, as its Eeyore stand-in, a donkey named Algore, a parody of...well, guess. The Brain quickly realizes that the rambling Algore is quite literally full of hot air, causing the occasional warm breeze. Cue jokes about Al Gore being the realcause of global warming.
In "Broadway Malady", The Brain's show, "Angst: The Musical", has a number called The Schadenfreude Polka. A musical with a number about Schadenfreude? How ridiculous.
True, each of them had female love interests, but a DVD featurette even acknowledged that the show was about the "love" between the duo (they were probably talking about platonic love, but it's easy to misinterpret that). And in the episode "Brinky" the two inadvertently mixed their DNA together in a cloning machine, essentially having a child with each other.
That whole episode played played up the couple thing past 11. They both fell into the family roles immediately and Romy addressed them as "my two dads". They went through all the cliche marriage problems of an after school special. At the end of it, Pinky asked Brain if they could have another. Why, even the episode title is a ship name: Brinky!
There's also the episode "Pinky Suavo", where Pinky, through an accident with Brain's "Personalitron", becomes a charismatic, suave, romantic figure loved by everyone. And we mean everyone. Watch Brain's initial reaction to the new Pinky and just try to deny that he's suddenly developed at least a mancrush on him.
For a brief moment in "You'll Never Eat Food Pellets In This Town Again", they sleep in the same bed.
Pinky also often dresses up as Brain's wife, neither can live without the other (as seen in "This Old Mouse" and "A Pinky and the Brain Halloween"), Pinky's given up his soul for Brain and Brain's given up the world for Pinky, and in "Just Say Narf" there's a scene where he actually tries to seduce Brain on a bench. Honestly, the sheer amount of Ho Yay moments with these two is staggering.
In the episode "Brain Drained", one of the interviewees suggests that the Pinky and the Brain TV show should drop the world domination aspect and be a Nick-Jr.-esque children's show called "Pinky-Winky and Brainy-Wainy".
Also, the songs in Elmyra's collection include "It's a Sugary Wugary Day" by Laffi and "Life's a Rosy-Posy Bed of Honey" by Mary Flewis and Porkchop. As Brain puts it, "The titles alone are enough to make my teeth rot!"
Tear Jerker: The Christmas and Halloween episodes.
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