Apocalypse's theme is a very regal piece that is absolutely appropriate for the resurrected pharaoh (particularly early on, when Apocalypse would just casually own whoever was fighting him without even lowering himself to speak as the music played).
The main theme was a remix of the 90's cartoon theme. They even played the 90s theme in a more straightforward way (albeit with acoustic Spanish guitar) in the episode where Spyke joined.
In "Retreat" we get a nice snippet of The X-Files theme to cement a joke that some guy named Mulder is a Bigfoot tracker.
is a very regal piece that is absolutely appropriate for the resurrected pharaoh (particularly early on, when Apocalypse would just casually own whoever was fighting him without even lowering himself to speak as the music played).