The show's intro jingle. It sounds so nefarious and is just oozing a feeling of "Screw everyone, let's get criminal!" And it works everywhere. Put it after any scene and it will still come across as epic.
The show's only use of the full theme, in the penultimate episode "Granite State", is perfect.
The narcocorrido 'Negro y Azul' played at the beginning of the episode of the same name.
Soundtrack Dissonance with the upbeat 'It's Such A Good Night (Scoobidoo Love)' used in a montage of Jesse selling meth all night.
The full theme is used at the end of the series' penultimate episode, "Granite State", as we see Walter go into full Heisenberg mode. It's a chilling scene as you see him get livid and then the cops come into the bar and we see his half-drunk glass sitting with his chair empty. The music only makes it that much more ominous.
The use of Tommy James' "Crystal Blue Persuasion" during the mass-production-of-blue-meth montage in "Gliding Over All"—not just the uncannily fitting title, but the easy, airy music fitting with the (presumably months of) relative halcyon days of Heisenberg amassing the bulk of his millions right before his retirement, and things ironically taking their final plunge south for Walt with Hank accidentally discovering who Heisenberg really was. The song truly gave us the feeling of Walt feeling he was "gliding over all" (in spite all that happened before and would start happening again very soon).
The use of Badfinger's "Baby Blue" as the closing song of the series, representing Walter's true love, his blue meth.
Fever Ray's "If I Had A Heart" in "Open House" really drives home Jesse's despair, and the song itself could serve as something of an ode about Walt.
"Freestyle" by the Taalbi Brothers, the badass Mexican guitar theme that plays in the Season 4 finale when Walt and Jesse burn down Gus' meth lab.
"Take My True Love The Hand" by the Limelighters, an easygoing tune that would be right at home in a Fallout game. Lyrically, it perfectly fits the scene in which it plays; when Walt treks through the desert with his barrel of money, the only thing he has left.