A great piece of music plays during the climax of "A Better World", when the tide of battle against the Justice Lords is turned by none other than Lex Luthor. The DVD commentary for the episode recalls the challenge in creating a heroic theme for Superman's most iconic villain. They succeeded.
The song that plays in "For the Man Who Has Everything", where Mongul trapped Superman in a fantasy Krypton. The moment when he heard Wonder Woman getting mauled by Mongul and turned to fight had the most awesome reprise of the theme song ever. Just before that, the scene where he breaks free of the dream of Krypton (and it explodes) is set to a heart-breaking reprise of that music from the start of his own series.
Batman singing Am I Blue? in "This Little Piggy". As an added bonus, there's no singing actor for him, it's Kevin Conroy singing! It's so awesome to the point that many people consider it to be better than other blues singers' versions.
Another great number from "This Little Piggy" is Circe singing Lulu's Back In Town at The Amphitheatre club in Crete. Needless to say, Rachel York puts on a great performance.
When the combined Lex Luthor and Brainiac are confronted by the Justice League, they summon seven earlier Brainiac models... and then change their minds to the tune of a wonderful dark reprise of the Justice League theme, as the Brainiac models change into the Justice Lords.
The music that plays when Superman delivers his Badass Boast to Darkseid, as well as when he delivers one hell of a Megaton Punch, featuring slowly swelling woodwinds and percussion that builds up into a euphoric, awe-inspiring crescendo as Superman unleashes the full extent of his power on an opponent that can take it. It's a Moment of Awesome with awesome music.