After escaping a hot-air balloon which took him out to a sea storm, Rocky is flying back to the shore, where he is mistaken for an enemy plane and shot at with flak cannons. In order to prove he isn't an enemy, Rocky flies in a certain pattern to spell out two words. Upon reading them, the general in charge of the air defences orders them to cease fire immediately. The words which Rocky spells out: US Taxpayer.
Ending up with Rocky getting a full escort of fighter planes.
The boat race between Rocky, Bullwinkle, Boris and Natasha, which goes from the lake in Frostbite Falls to smaller and smaller bodies of water, including puddles and irrigation creeks, all while Boris instructs Natasha to keep rowing and Bullwinkle keeps pouring water out of a bucket to contain a leak in his boat, actually a downed airplane.
Boris: Stroke stroke stroke!
Bullwinkle: Bail bail bail!
Then later when they sail at night in a fog:
Boris: Stroke stroke stroke!
Bullwinkle: Bail bail bail!
Boris: Stroke stroke!
Bullwinkle: Bail bail!
Bullwinkle: Hmm. There's quite an echo. Bail!
Bullwinkle: That's the first echo I ever heard that wrote it's own dialogue.
In another episode, Rocky and Bullwinkle are inside of an airplane falling out of the sky (surprisingly, this isn't the first time this has happened to them.) Instead of jumping out, they decide to find a way to keep the airplane afloat. Rocky comes up with the brilliant idea of using hot air, but where are they going to find the hot air they need? Rocky pulls out a copy of the US Congressional Record and tells Bullwinkle to start reading from it.
For those of you not in the know, the Congressional Record can be revised to correct "errors" by the politicians themselves. The "fixes" that can be implemented can be as egregious as adding whole new speeches or removing those in which the politician shot himself in the foot.
The government suffers another shot in the Goof Gas arc, when Boris and Natasha attend a congressional hearing. After the speaker has finished talking gubernatorial nonsense (Specifically, a statement that the government needs to remove the government from the process of running the government):
Natasha: Boris, what he said! You think he's already had Goof Gas?
Boris: Natasha, what he said, that is Goof Gas!
The reveal that Mr. Big is in fact smaller than Rocky.
The show's first real meta gag: after the mooseberry bush dies and Bullwinkle makes off with the mooseberries, only for them to (seemingly) explode and take Bullwinkle out with them, Natasha laments: "thirteen episodes worth of effort, wasted!"
The show has mocked itself several times despite its popularity. Below this paragraph is probably the most famous one from "The Treasure of Monte Zoom": What Rocky & Bullwinkle say after Boris & Natasha decide to use an A-Bomb to open the chest.
If we can put Fractured Fairy Tales here (since there seems to be no page for their funny moments), the entire "Riding Hoods Anonymous" episode is comedy gold. Especially the running joke about the basket full of (BOOM!) ...goodies.
Also in "Goof Gas Attack": "We'll declare war on EVERYBODY, but we won't tell ANYBODY!"
"It's... Time for Ding-Dong School!"
In the Mr. Peabody segment "Mati Hari", Peabody makes a pun and Sherman says that he should have saved that for the ending, to which Peabody remarks "I've got one much worse than that". At the end, Sherman groans at Mr. Peabody's ending pun, and Peabody says, "I warned you Sherman".
In the "Ruby Yacht" story arc, Rocky and Bullwinkle go to a library to research the ruby, and the librarian complains about that "noisy cat, always stomping around". The cat in question isn't making any noise.
An instance where the delivery kills it.
Bullwinkle: The rules clearly stipulate no human over ten can participate. I'm about as inhuman as you can get.
Rocky: You're a moose!
Bullwinkle: And that's another reason!
The recap in The Deep Six or It's Tough To Fathom has this exchange when recalling how the S.S. Plankton was over it's cargo limit and something had to be thrown overboard.
Captain: What'll it be? Passengers or lifeboat?
Narrator: Well, we couldn't get away with it on a kids' show, so it was the lifeboat they jettisoned.
In the prior episode proper (The Malady Lingers On or I Bought You Violence for Your Furs), the Captain still gave the option to either jettison the passengers or a lifeboat, and it was decided by a coin flip.
Bullwinkle is about to be thrown into a pit of cobras. He quips:
Bullwinkle: Too bad it isn't the end of the episode. We could use "Fangs For The Memories" as a title.
In the "Wossamotta U" arc, Natasha finds out Boris went to "college":
Natasha: Boris, you went to Penn State? Boris: No, state pen.
During the "Bumbling Bros. Circus" arc, Boris disguises himself as a kid so he can covertly feed the circus elephants reducing pills disguised as peanuts to make it look like Rocky's not taking good care of them, so he'll give up hope and leave. Bullwinkle can't quite get over the name he picked for his disguise:
Near the end of one segment,the Narrator is too busy laughing at one of his own corny jokes ("Tune in for our next arrowing episode...") to finish the outro, and an un-amused Rocky and Bullwinkle have to do it for him.
Bullwinkle: (ticked off) Oh, come on! It's the end of the episode! (Narrator keeps laughing) Rocky: (just as ticked) Oh, brother... Bullwinkle: The next episode is "The Flaming Arrow..." Rocky:...or "Bullwinkle Meets His Match!"
The "Upsidaisium" serial has General Broadbeam accusing Rocky of stealing the Upsidaisium payload (Boris did by impersonating Rocky). Rocky's alibi is that the General was with him the whole time. Broadbeam subsequently accuses himself, handcuffs himself and walks off saying "Come along, me!"
In the same story, Rocky has launched himself on a missile to retrieve the trucks filled with the Upsidaisium. Boris sabotages the missile causing it to veer off course:
Gen. Broadbeam: He's headed to Washington! Bullwinkle: Do you think he'll take the farm vote?
From "Painting Theft," where Bullwinkle says he sold 4,000 gallons of whitewash to some guys investigating Payola:
Bullwinkle: Believe me...to them it's just a drop in the bucket!
The Poetry Corner segment, where Bullwinkle attempts to recite the works of a certain Marshall Mathers the Third. He makes it through a few lines of Superman before stumbling across Eminem's trademark foul mouth in the book he was reciting from. He then flips through the rest of said book to find something less offensive to read from...then inevitably has to cut the rest of the segment short.
On the DVD, the outtakes of the last part of the "Goof Gas Attack" storyline, especially hearing the cast laugh everytime Paul Frees tries to say Peachfuzz's line, "Heavens to Eliza! He's a little fuzzy comet!"