"Tempus Fugitive" arguably has the most well-known CMOF of the series with this exchange:
Lois: If you wanna kill Superman, I don't know why you're going to Smallville or 1966.
Tempus: She doesn't know yet. Oh, this is good. This is really good. Um, Lois, did you know that, in the future, you're revered at the same level as Superman? Why there are books about you, statues, an interactive game. You're even a breakfast cereal.
Tempus: Yes. But, as much as everybody loves you, there is one question that keeps coming up: "How dumb was she?" Here, I'll show you what I mean. Look. (puts on glasses) I'm Clark Kent. (takes glasses off) No, I'm Superman. (puts glasses back on) Mild-mannered reporter. (takes glasses back off) Superhero. Hello! Duh! Clark Kent is Superman! Ha, ha, ha. Well, that was worth the whole trip. To actually meet the most galactically stupid woman who ever lived.
In "Ides Of Metropolis," Jonathan comes to see Clark, concerned that his mother might be having an affair with a younger artist with a covered painting as proof. When Clark tries to reassure him that just having a painting made isn't proof of anything, Jonathan unveils the painting right in front of Clark and reveals that it was a nude portrait. The look of Squicked out horror on Clark's face says it all.
Clark (in an almost squeaking voice): M-mom? (cut to opening credits).
Also in "Ides Of Metropolis," Lois and Clark go to interview Lex Luthor and find him skeet shooting off of his balcony... on the 110th floor of his building. When Clark asks him if he knows what could happen should he miss, Lex goes into a calm description of the lethal damage a falling clay pigeon could do before bragging that he never misses. At the end of the episode, we see him privately doing this again. He shares a good gloat over the episode's events with his butler, takes aim and... misses. With the funniest awkward-yet-still-somehow-stoic "oops" expression on his face as he watches plummet towards the unsuspecting public.
Lex: "Oops... Nigel? Call..."
Nigel: "The lawyers?"
Lex: "The lawyers."
Nigel (dryly): "Yes, right away sir."
In "I'm Looking Through You," Superman shows up at his own apartment to talk to Lois and claims that he ran into Clark at the courthouse. When the phone rings, Superman answers and proceeds to have a one-sided conversation with "Clark." After he hangs up, the scene cuts to a very confused Martha staring wordlessly at the phone.
From "Operation Blackout"
Clark Kent: Gee, Lois, if you were thirsty, all you had to do was say something.
Lois Lane: Clark, this isn't just any beer!
Clark Kent: I know. "It goes with sun and good times!"
From "Meet John Doe"
Malcom: Gotta go. Gonna jump to my death soon. Buh-bye.
The costume montage in "Pilot" (part 2). Most of them were flashy and ridiculous. All set to "Holding Out For a Hero" by Bonnie Tyler.
In "Man of Steel Bars", Superman, due to being accused of inadvertently harming Metropolis, is forced to go through police procedure and spend a night in jail. Absolutely nobody takes the idea totally seriously, not the judge, nor the cops nor Superman himself. The whole sequence is one long gag, with Superman's superstrength causing him to accidentally destroy every piece of equipment the police trying to get him to use - including shattering the ink table. It culminates in Superman taking his mug shot with a big goofy grin on his face, ending with a few good-natured posterity shots with a bunch of gleeful prostitutes and thugs.
In "All Shook Up", an amnesiac Clark sneezes, powerful enough to knock out a cab he and Lois rode in.
Cat's confession to the priest in "All Shook Up" which ends with her hitting on the priest and him running away.
In "The Eyes Have It," Clark has been blinded by the villain of the week. This leads to a scene of Superman saving a blind man, while pretending to not be blind, and then when the blind man asks to be pointed towards 56th Street, Superman just absentmindedly says "I think it's that way" and points before taking off.
In "Faster Than a Speeding Vixen", Lois imagines what her and Clark's already-busy lives would be like raising their children. A LOT of children. While Lois is trying to interview the Queen of England and the Pope, both whom are helping with the babies and couldn't even get a word in edgewise. Clark has to leave to avert a crisis and returns holding another baby, only to leave again and it starts over again. And each baby is named after Clark and Lois' family and friends (Jonathan, Martha, Lucy, Lana, Jimmy, Samuel, etc.). And one of them is developing super powers.
In one episode, Jonathan and Martha Kent are visiting Clark at the Daily Planet. At the same time, a sleazy politician running for governor is also at the Planet. He greets Clark's parents and promises to help fund Smallville's education system. As he leaves, Martha shouts to him, "You might want to start with geography! We live in another state!"
The Prankster caused some nice moments.
"Jimmy, give me back my dress."
"Now, there's something you don't hear in the news room every day."
Martha Kent's explanation on how Clark Kenting could possibly work as Clark is trying on tights.
Martha Kent: Well, one thing's for sure. Nobody's going to be looking at your face.
After the Arc Fatigue of the first wedding, which circled through clones, amnesia, and an alien invasion, the episode where Lois and Clark finally got married was titled "Swear to God, This Time We're Not Kidding."