The issue where Clark visits Luthor in prison, especially:
Lex Luthor: (to Clark, who's taking notes) The inimitable Lex Luthor opened the floor and shook hands with a baboon in a Superman suit... Next panel... Lex:(shaking a baboon's hand) Evening, Leopold. Leopold: Raark.
The fact that the Fortress of Solitude has a little welcome mat on the front door.
With a key hidden under it. A key that weighs half a million (500,000) tons!
Serves as a Brick Joke when the Kryptonian scientists use the Fortress while Superman is off-world. When he protests over the lack of respect to his privacy, they simply note he shouldn't have put his key in such an unsecure spot.
Atlas and Samson trying to woo Lois by, among other things, having an arm-wrestling contest with Superman.
The aftermath: a newspaper photo of them in the hospital, arms in casts.
Giving thumbs-up with their good arms.
When Lex is readied for the electric chair, he shoos the priest provided away because he "stinks of the irrational."
When Lex gains powers from the Superman serum a guard shoots at him with the expected results, but the amusing clincher is a bullet bouncing off his pearly white smile.
Luthor's subtle Take That to Moby-Dick in the prison issue: He programs his bibliobot to recite the book at the resonance frequency of his cell floor like a sonic drill, thus "boring [his] way out of prison".
Early in the prison issue, Lex notes that a majority of men subconsciously shape their eyebrows to the "Superman swoosh" out of internal desire to mimic him. During his fight with Parasite, Lex unknowingly wipes one of his own drawn-on eyebrows off. When Nasthalia notes it, Lex quickly redraws it back on... except now its an over the top imitation of the Superman swoosh. The fact that his other brow looks normal (and obviously meticulously drawn to NOT look like Superman's) makes it look like he's perpetually giving the the People's Eyebrow.
The Running Gag throughout the series that - even when confronted with clear evidence that Clark and Superman are one and the same - nobody believes that Clark and Superman are one and the same.
Lex Luthor (after being blasted by a very Superman-y Clark Kent with a Gravity Gun): Kent? No. Hmm, now there's an amazing idea. I should be writing these...
Even when he confesses to Lois in Issue 2. She still doesn't believe it all the way up to the final page.
A meta one: in the behind the scenes commentary on the book, a rough version of this cover◊ can be seen, only with the Earth replaced with a basketball.