In "House of Crime", a clue states that the guy who's kidnapping everyone has a grudge.
Donald: What!? I don't hold a grudge? (everyone looks at him suspiciously) What?
(scene transition; Donald is locked in the elevator)
Donald I WANT A LAWYER!!!
The Running Gag of Donald following an annoyed Goofy shouting "Everybody loves me! I never get mad!".
Max nonchalantly asking the Phantom Blot if he can park his deflated blimp.
Another running gag involves Donald getting trampled by a gaggle of Disney characters in several episodes.
In "Donald Wants to Fly", Donald dons a pair of donkey ears and dubs himself "Donald Donkey" because donkeys can't fly. Cue the flying donkey from The Three Caballeros.
King Larry messing around with Horace's controls in "King Larry Swings In".
The crew reminding Donald what happened the last time royalty visited the club. (Donald accidentally dropped baby Simba).
In "Gone Goofy", Mickey asks Donald if he's going to give Goofy a (literal) pink-slip to get him fired, Donald hesitates for a moment before shouting yes.
The Pink Elephants decide to perform in the House of Mouse. Hilarity Ensues:
One of them drinks Clarabelle's drink, and she says "What'll I do? What'll I do?" Then cut to Timon pointing at the elephant's rear saying "What an unusual view." And then the elephant kicks him away.
In the midst of it all there's a shot of an elephant acting as a canoe with Pocahontas in it, Hercules struggling to lift the elephants, and another elephant dancing with Ursula before tossing her on top of Goofy.
Timothy just holds out a sign that says "Boo!" and they vanish.
In "Clarabelle's Big Secret," Chernabog's cameo where he reveals he's afraid of the dark. Let that sink in: Satan is afraid of the dark!
During "Where's Minnie?", when Daisy is left in charge of the club while everyone else searches for Minnie, we get this exchange:
Daisy (introducing the next segment): "Usually we'd show a cartoon here, but instead I've got an act! It was written by me, stars me and guess who's in it: me!"
Mortimer Mouse (in the audience): "Quit threatening us already and show the cartoon!"
Said act turns out to be an affectionate parody of Davy Crockett.
In the pilot episode when Donald takes over the House, he keeps trying to rename the place to "House of Duck", only to instead be given plaques reading "House of Muck" and "House of Yuck", ending with... "House of Pancakes".
Donald sleeping on the job while Oysters hop right over him in "House of Genius"
In the same episode, Goofy asks Captain Hook if he'll like deep-dish or pan pizza. Hook's response is "Bring me PAN!"
The robot Donald's clear way of speaking, introducing himself as "Duwwod".
In "The Stolen Cartoons", Mickey is feeling slightly stressed, so Minnie suggests he has a drink. Cue Mickey taking a drink out of a rather large pet water bottle.
In "The Unplugged Club", Mickey is stressed and Minnie asks him "Do you need a timeout in your wheel?" Then we see the single biggest hamster wheel in history.
"House of Scrooge" begins with Scrooge walking up on the stage and berating Mickey's act. When Mickey asks what he's doing there, Scrooge informs him that he bought the House of Mouse. Cut to Donald, who facepalms.
And right after there's this exchange:
Mickey: "You can't buy the place! Pete owns it!"
Scrooge: "Everyone has their price."
<Pete drives up in a golf cart out of nowhere, dressed like a pimp and lugging around a gigantic bag with a dollar sign on it>
In "Big Bad Wolf Daddy", Mickey complains about having to fire O'Malley and the Alley Cats, asking Donald if he has any idea how angry a cat would be to be fired by a mouse. We then cut to Thomas O'Malley, who calmly says "Show biz. It happens."
Aside from Mortimer's failed attempts at hitting on the guests, "Goofy's Valentine Date" also has the disclaimer for the commercial at the end of the short.
Announcer: Dealing with the Queen of Hearts may be hazardous to your head.
In "Clarabelle's Big Secret", when Mortimer snarks about Clarabelle's gossip, he first asks if her next secret is that "Rafiki is old". Timon laughs at the statement and Rafiki responds by hitting him on the head. Later, Mortimer makes the same remark, only this time joking that the secret is that "Snow White is the fairest of them all". Timon laughs again, this time getting hit by the Evil Queen.
Some of the secrets she finds out about the guests, the best one probably being the White Rabbit's.
White Rabbit: I'm not really late! And I don't have a date! I'M A FRAUD!
The announcer saying that Donald Duck is prone to hissy fits and temper tantrums at the end of "Everybody Loves Mickey".
The Running Gag in "Chip n Dale" with Pete being unable to open his bag of nuts and everyone he asks to open it screwing him over instead.
Ranger Woodlore always being there to scold Humphrey the Bear for his actions in "Humphrey in the House".
"Pete's Christmas Caper" has a couple, both involving Mortimer. When Mickey goes asking people what they want for Christmas, Mortimer appears in the video asking for Minnie's phone number. He appears a second time with a black eye, this time asking for Daisy's phone number. After that, he appears once more with bandages on his head, this time asking for a doctor's phone number. Aside from that, Mortimer's failed attempts at kissing Minnie under the mistletoe are also pretty humorous, especially when his last attempt ends with him getting kissed by Pete.
The Running Gag of Mortimer trying and failing to get Minnie to kiss him under the mistletoe returns in "Clarabelle's Christmas List".
At the end of "Pete's House of Villains", he's forced to clean the place up. As he's scrubbing the floors dressed in Cinderella's "maid" outfit, Lady Tremaine (Cinderella's stepmother) appears behind him, looming over him with that same smug grin she uses when she makes her stepdaughter miserable. Pete is creeped out as she's doing this, and nervously laughs as he tells her to quit staring at him.
The scene in "Pluto Saves the Day" where Pete, disguised as Snow White, tries to give Goofy a sleeping apple.
Pete:(falsetto) Oh, Goofy! I have a delicious apple for you.
Goofy: No thanks. Ma said never to take fruit from a stranger.
Pete: But I'm Snow White.
Goofy: Yeah? Then who's that? (points to the real Snow White sitting at her table)
Pete: Uh, well, y'know, uh...An apple a day keeps the doc away.
Goofy: But I like Doc. (holds up Doc)
Pete:(angry; normal tone) Just eat dis apple!
Goofy: Okay, Snow. Betcha Prince Charmin' never saw this side of ya before the kiss. (Pete shoves the apple into his mouth)
After spending the whole entire episode being trolled by the Aracuan Bird in "Donald and the Aracuan Bird", Donald finally snaps and takes off after the bird with a gradually increasing amount of tranquilizer guns. In the ensuing chaos, everyone in the house except the Aracuan Bird (including Mickey and Donald himself) is knocked out...exceptPrincess Aurora, who is sitting there wide awake and annoyed among the sleeping masses.
"Pete's One Man Show": To disguise the fact that there's no audience, the gang puts up cardboard cut outs of well-known Disney characters and hide behind them, shouting their catchphrases. Cue Goofy as Dumbo:
Goofy: Be our guest, be our guest!
"The Stolen Cartoons": Mickey and Minnie find Horace tied up in the control booth.
Mickey: Horace, what's wrong?!
Horace: All the rainforests are bein' chopped down, nobody votes anymore and the Internet's too dang slow!
"Ladies Night" starts with Clarabelle and Daisy talking about finally getting to do the things they want to do. Clarabelle especially has her mind on one thing only...
Daisy: We can finally do a show with things we like!
Speaking of Eeyore, the bit where Goofy rearranges the seating so the guests can make new friends. Eeyore is paired with the overly-positive Jiminy Cricket, Bambi is paired with the hungry Big Bad Wolf, but the icing on the cake is the Mad Hatter paired with...Judge Claude Frollo.
The entirety of "Donald's Goofy World", where Donald has a nightmare that everyone and everything is turning into a clone of Goofy — including his neighbors, friends, animals, plants, TV shows, even the Sun, and eventually Donald himself. The whole thing is so absurd, it's hard not to laugh.
The entirety of "How To Be A Gentleman" (3:36 at the link). The ending, where Goofy beats the narrator up with a club after he berates him for forgetting his pants, doubles as Goofy's Moment of Awesome.
On that note, we have Goofy greeting The Queen of England:
Goofy: HIYA QUEENIE!
(Queen hits him with her scepter)
Goofy: Hey, Liz?
(Queen hits him again)
Goofy: Your Royal Pain?
(Queen hits him again)
(Queen hits him again)
Goofy: All I said was ouch!
(Queen hits him some more)
Narrator: One should bow gracefully and say, "my dear Queen, how delightful to make your acquaintance".
(Queen hits him so hard that he falls and a lump grows on his head...and several more lumps grow from said lump)
In "How to be Groovy, Cool, and Fly", the narrator insults Goofy's wardrobe by saying that he looks as if his mother still dresses him. Suddenly, Goofy's mother appears and tells her son that he forgot his hat.
"Goofy's Big Kitty" has two. The first one is Goofy using his belt as a collar for the mountain lion he mistook for his new pet cat, which results in Goofy using the small collar to hold up his pants, giving him a feminine shape and comenting on his hourglass figure. The second one is when the mountain lion gets away, causing Goofy to break down in tears and scream "I'm a terrible father!"
In "How to be a Spy", when they go over "Debugging", Goofy starts to swat bugs crawling out of a phone while screaming "Bugs in my phone!" During this, he briefly stops to say "Dumb joke".
"Car Washers" ends with Mickey telling Pete that his car Shrunk in the Wash. Pete is incredulous of this, but then he ends up forced through the car wash and becomes tiny, yelling at Mickey, Donald, and Goofy in a high-pitched voice.
In "Mickey and the Color Caper", we see a picture of the Phantom Blot's parents, and the picture resembles the famous painting American Gothic.
Goofy arguing with himself over the phone in "Locksmiths".
All of The Nutcracker. It's a fairly faithful retelling of the tale, but almost every second is a riot with the Interactive Narrator (John Cleese, no less), from kicking God papa Drosselmeier (Von Drake) out of the story for breaking the nutcracker, refusing to help Mickey (playing the nutcracker) explain to Goofy that he needs a role to be in the story, and telling Donald (playing the mouse king) that the character will win.
The animatronic parrot giving a Wolf Whistle after Mickey and Minnie kiss at the end of "Mickey's Pinball".
At one point in "Housesitters", Mickey, Donald, and Goofy shoot at Pete and cause his buttons to fall off. The trio's reactions to the buttons for the dropseat of Pete's long johns getting shot off are hilarious.
In the "Time Reverser" Ludwig Von Drake short, the professor attempts to test the titular time machine by breaking his mother's china and then going back in time to prevent himself from doing that. However, the time machine ends up breaking, resulting in an understandably horrified Professor Von Drake hurriedly leaving to buy new china while his mother hollers his name in anger.
Yet another Ludwig Von Drake short, "Teledinger", consists of Ludwig inventing the telephone and a flashlight without realizing that those things already exist.
A third Von Drake short, "Money Increaser", shows the professor inventing a money-increasing machine to save others from poverty, only for it to get him arrested for counterfeiting.
"Computer.don" has Donald's Imagine Spot of Daisy dumping him for a robot and Mickey's cameo where he is mistakenly packed as the mouse for Donald's new computer and storms off while yelling that he isn't supposed to be in this cartoon.
Mickey's ridiculous procrastinating on his piano practice in "Mickey's Piano Lesson". The piano instructions being named "Easy as Pie" lead to him eating some pie, he then decides to go on a picnic, and after that goes sky diving, during which Minnie calls him to see if he is practicing. What's especially funny is that when Mickey looks at the instructions again, he nearly repeats the cycle until he realizes how much more time he would waste.
In "Double Date Don," Clara Cluck is seen watching television and the announcer says "We now return to The Lame and the Whiny!"
In the same short, Clara tries getting Donald's attention by throwing herself into the sea tied to his bricks. As he brings them back to the shore:
In "How to Be Smart", Goofy gets a crash course in grammar:
Narrator: A sure sign of smarts is one's ability to write, and the beginning writer is wise to choose a simple sentence. (Ludwig Von Drake brings up a sentence on a blackboard) Goofy:(reading message) "I am smart." How about that? Narrator: The writer can bring more meaning to the sentence with the addition of an adverb. (Von Drake changes the sentence) Goofy:(reading) "I am not smart." (offended) Hey! Narrator: A conjunction allows an additional sentence segment to be linked. (Von Drake changes the sentence yet again) Goofy: "I am not smart and I smell." (infuriated) You little...! Narrator: Don't be afraid to use other nouns as descriptors in your sentence. (Von Drake changes the sentence yet again) Goofy: "I am not smart and I smell like a monkey." That's it! (he chases Von Drake, only to slip and fall down) Narrator: Remember that sometimes the best sentence is the shortest. Goofy:(a new message displayed) "Ouch!"
"How to Be A Waiter". All of it. Notable examples include Goofy practicing emotions up to "Unconsciousness" (he gets knocked unconscious due to practicing in a fast pace) and reciting a tongue twister ("How much wood could a woodchuck chuck if a woodchuck could chuck wood?") in different voices (and in Japanese!).
The end of "Mickey's Mix-Up," when the fax he initially sent to Mortimer winds up in the hands of Roy E. Disney, then-Chairman of Walt Disney Feature Animation.
Roy E. Disney: (after reading the fax) "Huh? What'd I ever do to him?"
The fact that Roy Disney sounds more confused than offended.
In "Whitewater Donald", Donald brings Daisy along on a fishing trip, because he forgot he promised her a romantic date an thinks he can do both, but Daisy keeps interrupting his fishing with various 'romantic' requests like serenades, rubbing her feet, etc. When she wants him to read her a poem, we get this:
Donald: "Roses are red, violets are blue, LET ME FISH!"
"Bird-Brained Donald" in general is a pretty funny short, but the highlight is definitely the completely out-of-nowhere Disney Acid Sequence in which the Aracuan Bird takes multiple pictures of Donald.