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!
Also a Mythology Gag, as Lois refers to the giant "airline marker" key to the giant door back in the Silver Age continuity.
Atlas and Samson trying to woo Lois by doing, 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.
in the animated film version, once 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".