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The episode "But That's Not All, Folks!" where Pinky and The Brain transmit a live infomercial. Some of the skits they do are interesting.
Even the series with Elmyra actually had something this troper thinks is pretty dang funny: The episode where Brain does his own version of Mr. Rogers' Neighborhood has a scene where his name is the secret word that causes bells to ring and red lights to flash. But when Pinky shows up:
Pinky: Hello, Mr. Loyal Subject! Hello, Brain! [lights flash] Brain: You said the secret word! Pinky: I did? Um... what's the secret word, Brain? [lights flash] Brain: You said the secret word again! Pinky: Really? I've never won anything before. What do I win, Brain? [lights flash] Oh, this is so exciting! Brain: OK, that's enough. Pinky: Enough of what, Brain? [lights flash] Brain: Stop saying the secret word! Pinky: What's the secret word, Brain? [lights flash] Brain: Errrrgh! Stop saying "Brain"! [lights flash] Pinky: Ah! You won, Brain! [lights flash] Brain: Stop it, stop it, stop it! Pinky: Stop what, Brain? [lights flash] Brain: Okay, that's it! The secret word is not "Brain"! Pinky: Wuhahaha! Shut yer face! Shut yer face, Brain! [continues to repeat "Brain", with the lights flashing each time, until Brain hits him on the head with his sceptre] Brain: The new new secret word is "pain".
There's also this exchange from the episode where Elmyra takes them on her class's field trip to Duckyland:
Brain: Hey, where's Elmyra? Pinky: Oh no, she's lost! We might never see her again! Brain: Stop trying to cheer me up, Pinky. She's got the tape.
There is also the funniest variation of their closing line, after Pinky fouled up Brain's attempt to win a horse race:
The Brain: Quiet Pinky, I'm getting ready for tomorrow night. Pinky: Why? What are we going to do tomorrow night? The Brain: [Irritated] Guess! Pinky: Oh, try to take over the world, right.
In All You Need Is Narf'...
Yoyo Nono: You look so sad. I will sing you my happy song. EEEYYYAAAOOOEEE!!!
Then a few more times after:
Yoyo Nono: I will sing my beautiful song. EEEYYYAAAOOOEEE!!!
Yoyo Nono: Oh, then I will sing my sad song. EEEYYYAAAOOOEEE!!!
Yoyo Nono: I will sing my love song. EEEYYYAAAOOOEEE!!!
And then again on the TV: EEEYYYAAAOOOEEE!!!
The cartoon that is completely from Pinky's POV.
This basically explains how Pinky comes up with his non-sequitur answers to Brain's famous question.
From That Smarts...
Brain decides that Pinky has become smarter than he, and to balance the group he must become the dumb one. Cue his Oh, Crap face right after he realizes Pinky has just done the same.
This beautiful moment from Welcome To The Jungle:
Snowball: I have a joke for you, Pinky. Knock knock.
Brain: Pinky, that's absurd! You are nothing of the kind! [The clone's] chromosomal make-up just happens to include both of our genetic building blo- *beat* AAAAHHHH!!! Oh my Lord, you are its mommy...
This exchange from "The Pinky Protocol":
Pinky: "I see an angel coming for us out of the sky."
Brain: Are you pondering what I'm pondering? Pinky: Phew. Oh, I'd say the odds of that are terribly slim, Brain. Brain: True. Pinky: I mean, really, when have I ever been pondering what you've been pondering? Brain: To my knowledge, never. Pinky: Exactly. So what are the chances that this time I'm pondering what you're pondering? Brain: Next to nil. Pinky: Well, that's exactly what I'm thinking, too. Brain:(realizing) Therefore, you are pondering what I'm pondering. Pinky: Poit! I guess I am.
When Brain tries to make mice the dominant species on earth so that they'll elect him as their leader.
Pinky: Egad! Brilliant Brain! Oh wait-no, no. Why would they pick you?
Brain: Because I'm very likeable.
From, "The Visit":
Brain: Pinky, my parents are driving me crazy.
Pinky: Really? Well, that doesn't leave with me much to do.
The writers may have called "Yes, Always" a very expensive inside joke, but it's still a hilarious one for the viewers that do get it. The best part, though, isn't spoofing Orson Welles' commercial taping:
Producer: Brain, you're here, great! And only 45 minutes late today!
Pinky's mother and father (both voiced by Eric Idle) have some hilarious moments, but he highlight is when they're packing to go to New York, and Pinky's mother is stuffing her suitcase full of food pellets.
Pinky's Mother: I'm almost packed! We'll have food pellets for lunch, food pellets for supper, then for breakfast I thought... food pellets! Brain: I'm told they do have food in New York. Pinky's Father: Where is this New York? Is it far outside the cage? Brain: It's very far away. Pinky's Mother: Ooh, I'd better take some food pellets then! Pinky's Father: As far as that sink? Brain: Much, much father. We have to take a plane. Pinky's Mother: A plain what? Brain: An airplane! It's, uh, a giant metal bird. Pinky's Father: Bird?! Where?! Run! Pinky's Mother: Ah! Giant bird!! Brain: It's not a real bird! Pinky's Father: A bird'll swoop down and eat you right up, he will! Pinky's Mother: Unless it's a llama! Pinky's Father: I know — we'll feed it food pellets! Pinky's Mother: Food pellets? Where will we get food pellets? Pinky's Father: ...I don't know.
Well I think so Brain, but what if The Hippo doesn't want to wear a Thong?
There's an episode (Animaniacs Stew) where Brain gets paired with Mindy instead of Pinky. He gets chased by a riding lawnmower, and tries to escape it by climbing the side of a tree. The mower simply runs right up the side of the tree after him. Seeing this, Brain looks at the camera, and deadpans "This is most unexpected."