Anti-Climax Boss: The story seems to be building towards a major confrontation between Superman and Brainiac, but Brainiac is ultimately defeated by Lana, whose Mercy Kill of Lex robbed Brainiac of a viable host. Instead of a great battle, Brainiac simply breaks down at Supermanís feet. Superman's true greatest threat is evil!Mxyzptlk.
Complete Monster: Brainiac. He brainjacks Luthor in the most horrifying way possible, murders most of Superman's remaining friends, and is completely devoid of anything resembling a conscience.
Continuity Lockout: Shades of this, since it references Superman's history, both famed and obscure. However, that's the entire point of the two-parter, to briefly touch on the Superman mythos. Do you really have to have read the Jimmy Olson book in which he became Elastic Lad to enjoy the story?
Evil Is Cool: Despite appearing in a few panels, Moore's revision of Mr. Mxyzptlk, has remained an iconic rendition of that character. Post-Crisis authors increasingly nerf him because Moore demonstrated quite successfully that the Fifth-Dimensional being is capable of being Superman's worst enemy.
Harsher in Hindsight: The Prankster and Toyman were re-imagined as psychopaths in the Post-Crisis universe, making their decision to get back at Superman by murdering Pete Ross and outing Superman's secret identity more disturbing in retrospect.
Batman and Robin attacking Brainiac's energy shield with sticks.
After Brainiac attempts to continue the battle by taking control of Luthor's corpse, in one panel it looks like Luthor is making a derp face.
They Wasted a Perfectly Good Character: Lex Luthor, Superman's greatest Arch-Enemy, the greatest criminal mind of our time, is reduced to a meat puppet in his final (Silver Age) appearance. THAT'S how Lex Luthor goes out. Moore does treat him respectfully by noting that Superman considers him and Brainiac his two greatest threats, but Brainiac is shown as Eviler Than Thou and then Evil!Mxy comes in and steals the show.