These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Not to mention: Pinky is much more literate than Brain.
Word of God has confirmed that the theme song leaves it open to the viewers to decide...
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 Re Tool.
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.
The Mask of Lillith and the symbol of Seele, from Neon Genesis Evangelion made its first appearance on one of Brain's diagrams. Especially since it was done in 1993, two to three years before it actually showed up.
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.
Magnificent Bastard: Brain on occasion. Usually when he's trying to save the world for a change.
Memetic Mutation: It is difficult to say "What are we going to do tonight?" to someone who watched this show without getting "The same thing we do every night, try to take over the world!" as a response.
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!"
The Woobie: In spite of his cheerful personality, Pinky is definitely one of these. He gets hit with Break the Cutie quite a bit (Like when he was crying in "The Family That Poits Together, Narfs Together" when he remembers being taken away from his family) and he could really use a hug in the Christmas and Halloween special episodes.
Jerkass Woobie: Brain has his moments, particularly when he realizes how bad he hurts Pinky and gets upset about it.