Jake: Uncle Charlie says I don't have to tell you.
In episode 3, when Alan mentions visiting Disneyland:
Charlie: Alan, I'm not thrilled about having one small rodent in my house. (Jake's guinea pig) Why would I drive fifty miles to see their kingdom?
Episode 7, Judith accuses Alan of speaking derogatory things to Jake about her.
Judith: Alan, have you been badmouthing me?
Alan: B-B-Badmouthing you? To whom?
Judith: To Jake.
Alan: Oh, to Jake. No, why?
Judith: His attitude towards me lately is so disrespectful. I have to wonder where he's getting it from.
Alan: Well I can assure you that I always make it a point to speak highly of you in front of our son.
Judith: What about your brother?
Alan: Oh, with Charlie I'm completely honest.
Judith: That's not what I meant.
Alan: I know. Smug grin
Charlie walks into the scene, holding a bottle of beer.
Charlie: Hey Judith.
Judith: Charlie, have you said derogatory things about me to Jake?
Charlie: No why, did you want me to?
Judith: I don't why he's acting this way, avoiding me, ignoring me, acting like I'm the enemy.
Charlie: But you get why I'm doing it, right?
Episode 13: Judith stays at Charlie's due to an earthquake in LA that hit her house hard. Alan ends up staying there briefly due to jealousy and then Charlie and Alan make a plan to get her out by making Judith jealous. When Judith meets Alan's date, Charlie plays certain notes on the piano in response to what's said. When Judith leaves, he plays Na Na Hey Hey Kiss Him Goodbye's chorus.
Made even better when the voices that usually chorus "mennnn" during the scene changes say "squab" instead.
Episode 14: Alan pretends to not be home when Judith arrives, followed by Charlie's answering Judith's questions with commentary from the Animal Planet. When Judith leaves after bitching about Evelyn, Charlie says "I'll tell Alan you stopped by." just to piss her off a bit more.
Alan is trying to get Jake to study for his history test, Charlie walks in drunk and ends up unintentionally helping Jake study for it by making it a pop quiz.
Not to mention Charlie asking Alan to drive him to the local 7 Eleven so he can get some snowballs and an eskimo pie.
Season 2 finale, after Judith's done her typical threat of legal consequences because of Jake's behavior for giving her a $25 chip from Caesar's Palace that he won from Charlie, Charlie and Alan mock Judith in high pitched tones that just sells the scene.
Episode 2, Alan needs Charlie to be his receptionist for the day so he can stop Jake getting expelled from school. Charlie with a lot of caffeine in his system when they're in the car tapping a song and making suggestions for how to make money in traffic jams is hilarious.
Episode 5, Alan calls Charlie a misogynist, you think he'd respond with some witty response, instead he grabs a dictionary.
One of Alan's finest would be him naming off movies in a movie trivia game but adding "Blow it out your ass!" during a meltdown of his in "That Special Tug".
Really, the entire episode qualifies as a CMOF. Did you forget "There's not enough bowel movements left!"?
Charlie's showing Alan how their mother can make any good thing bad and is later proven right.
Alan states that "I need to communicate after lovemaking. I need to share!" after a chat with his girlfriend Kandi proves to be rather...silly.
Charlie: Well maybe you should've thought of that before you started boinking a girl with the IQ of Tickle Me Elmo.
The entire opening scene in "Don't Worry, Speed Racer," but especially:
Alan: Look, Jake, it, it, it— it's not that you have to be particularly smart to have sex.
Berta and Charlie: Yeah, look at your dad!
Not to mention...
Charlie: Really, how much more damage could we have caused?
Alan at least tries to pretend to be happy for Judith when he learns that she is getting remarried. As soon as Judith leaves, though...
Charlie: Five, six, seven, eight...
Alan:*Conga* No more a-li-mo-ny! No more a-li-mo-ny! No more a-li-mo-ny!
Alan [to Judith on the phone]: I'll tell him [Charlie] to keep his hands off Myra. And then, I'll tell the rain not to fall, the earth not to spin, and you to STOP NAGGING ME! [hangs up] Oh, boy, I'm gonna pay for that.
Berta: You know what your problem is? Phone cojones.
Alan: Excuse me?
Berta: When you're on the phone with her, you got boulders between your legs. The minute you hang up, you're as smooth as a Ken doll.
Charlie whilst he's drunk at the start of S04 E22, mostly the inability to unlock the front door.
Charlie: Oh hey Alan, come on in!
Alan: Why don't you come in?
Charlie: I can't...I lost my key.
Charlie's blackout chilli.
Alan trying to get Charlie to help Jake with his book report.
Charlie: Relax, I'll take Jake to the DMV to get his license.
Charlie: *Holding up a can of beans* Beaaans!
Charlie's balls are on fire due to some stuff he used to get the grey out of his pubic hair.
Indian doctor: We have a saying in my country. "You can put a tuxedo on a goat, but still a goat. "
Charlie: Yeah, well, we have a saying in my country, too: "Help me, my balls are on fire!"
Jake sneaks out to go to a concert and sneaks back in with a drugged up Charlie. They get caught by Alan.
Alan: [to Jake] Do you have any idea how much trouble you're in?
Charlie: I do not. Do you have any idea how beautiful you look in that light?
Alan: I'm not talking to you.
Charlie: Yeah, well, I'm not talking to you either, except for right now, this is me talking to you, but, no longer. [makes pop sound]
Alan: Would you please just... go to sleep?
Charlie: Okey-dokey. [grabs pillow and goes out of view]
Alan [to Jake]: You and I have some talking to do.
Charlie: Will you make up your freaking mind?
Charlie has to give a concert as Charlie Waffles, he finds the solution to his stage fright.
Charlie: Hey, Alan, I figured out what went wrong in seventh grade!
Charlie: I hadn't started drinking yet! [walks in drunk]
Alan: Charlie, you have to get out there.
Charlie: Right, the little bastards await.
Alan summarizing the majority of the series when Charlie sleeps with someone that's connected to someone important in his life.
Charlie: How could you take the fall for me?
Alan: I don't know, but it always seem works out that when you get laid, I get screwed!
Charlie's cooking in episode 3, particularly the cinnamon buns tube.
Charlie: I christen thee H.M.S Kitchen Table, godspeed.
Charlie hits the tube on the kitchen table three times and it doesn't open.
Charlie: I think we have a bad bun tube.
Alan: Here, give me that.
Alan hits it on a kitchen bench and opens it
Alan: Just gotta know how to wack it.
Charlie: I bow to your superior expertise.
Charlie tries to help out Miss Pasternak get back on her feet after what happened the last time they met. It ends the exact same way.
It's horrible on Charlie and Alan's part, but their threatening Jake with military school is just hilarious. (He's not going to military school.)
Episode 8, Charlie catches Jake licking his piano after getting grounded for mooning some girls.
Charlie: What are you doing?
Jake: Playing 'Smoke on the Water'
Charlie: With your tongue?
Jake: Pretty cool, huh?
Charlie: That's not cool, it's disgusting. Alan, get in here! [Alan comes in] Your kid's licking my piano!
Alan: Jake, don't lick your uncle's piano.
Jake: But I'm bored.
Alan: Go read a book.
Jake: I don't wanna read a book.
Charlie: Then go lick a book! [Jake leaves] How long is this whole grounding thing gonna go on for?
Alan: Two weeks.
Charlie: Two weeks?
Alan: Charlie, he stuck his ass out a bus window at the girls' track team.
Charlie: That's what you're grounding him for? When you were his age, you mooned the girls' choir.
Alan: No, uh, when I was his age, you pantsed me in front of the girls' choir.
Charlie: Oh, right. Well, either way, you made the yearbook.
Charlie, Alan, Herb and Jerome's discussions about when they first started dating, first time they had oral sex and when Gordon the Pizza Guy shows up, the names that their penises are called.
Herb high on pain killers at the hospital after he hurt himself when Judith's water broke and then when he sprained/broke his arm. It works thanks to Ryan Stiles' acting.
Episode 3, Jake asks Charlie to drive his car.
Charlie:You want to drive my $80,000 car?
Jake: Yes please.
Charlie: It's a good thing he's polite, it's a necessary quality in a doorman.
Jake: Is that a yes or a no?
Alan: That was a no.
Jake: And the doorman thing was an insult?
Jake: Oh. [Jake leaves the kitchen.]
Alan: And a prophecy.
Episode 5, Charlie tries to kick Alan out of his own car.
Charlie: That's it, get out!
Alan: It's my car!
Charlie: Fine, how much do you want for it?
Followed by Alan and Charlie are trading insults by going through the alphabet (which they call a "word game"). Especially when Charlie says Alan is a vagina, but when Alan challenges it Charlie changes it to 'vagina adjacent.'
Charlie joking in "Warning, It's Dirty" that since Alan's been living with him for seven years, they're a common-law couple. Legendary TV Producer Marty Pepper visits with Evelyn (She wants to sell his house.) and he lampshades the theme of the show.
Charlie spends an episode writing a theme song for a cartoon on Nickelodeon called Super Dad, he uses the "Super Dad" part to describe Alan's parenting when he acts like a hypocrite, then later in the episode, he gives some girl advice to Jake and does a piano riff and says "Super uncle!".
Charlie takes pot and ends up hallucinating past one-night stands... and ZZ Top.
Charlie, after waking up on the stairs, pantsless, asks himself What Did I Do Last Night?? Roberta finds his pants in the mailbox, with many stamps stuck to the seat. Later, this conversation ensues:
Jake: Oh yeah, and I saw Uncle Charlie trying to mail his pants.
Charlie: Wait, you saw me do that?
Charlie: And you didn't ask why?
Jake: Over the years, I've learned to just look the other way.
Charlie: Hey, there's a note in the pocket! (reading note) Dear Inspected by #94, it is with a heavy heart that I must write to you that the zipper you have signed off on is unsatisfactory. The reason is it has gotten caught on my ballsack, so I am sending them back. I hope you are able to remedy this situation. Sincerely, Charles Francis Harper. Huh, that explains the blood on my shorts... I hope.
Episode 2, all of Charlie's antics to get Alan to move out. Including Larry the cockatoo, sitting on Alan's toilet whilst Alan's in the shower and then getting in the shower with him.
Episode 14, Jake and Eldridge's Jack Ass Expy antics.
From "Big Girls Don't Throw Dog Food" Alan finds himself back in his old room after he asks Walden if he could stay, “just a couple of days until I can find my own place,” and finds himself in a battle with Berta as to whose room this now is. Walden explains, “Yes I told him he could stay for a couple of days,” to which Berta informs, “This guy is like genital herpes, once ya got ‘em, ya got ‘em for life!”
Episode 908, where Alan slowly transforms into his brother. At the end, he gets checked into a mental hospital, calls hotel room service with an imaginary phone, asks for Asian hookers, and at the end, lays back, and says "Winning".
Episode 909, with Alan's life rapidly becoming worse & worse after his leaving rehab. Of particular note, is Walden walking into the front lounge with Judith's daughter & asking if anyone else has noticed how much she looks like Alan, and the immediate Oh Crap reaction that Alan & Judith both have.
Zoe when high on pot brownies.
Kathy Bates (yes, ''that'' Kathy Bates) starring as Charlie's ghost in Alan's morphine-induced hallucination.
In the season finale, as Jake graduates high school & heads off to the army, he tells his worried parents "Don't worry about me, worry about our nation's enemies." After Jake leaves, a moment passes, before Walden chimes in.
"I am worried."
Walden's birthday present for Ava.
The "You're a Douche" musical number in Walden's head, a rare high point in the newer series.