The Eva movies utilized music so well, there are so many scenes to list:

Air: (SPOILER)The Bach tune that plays while Asuka slaughters the Eva Series.
Komm Susser Tod (come sweat death): (SPOILER)The theme that plays when Shinji strangles Auska. Also the “end of the world” theme.
Expansion of Blockage: (SPOILER)The BMG that plays when Shinji rejects instrumentality, and Lilith falls to pieces.
Jesu, Joy of Man’s Desiring: (SPOILER)Another Bach piece that plays when the ‘live action’ section of the film begins.

Opening of a Dream: (SPOILER)Plays when Shinji finally gives up his mother.

Ode to Joy: (SPOILER)Everyone MUST know this one. It’s used rather unconventionally in Death and Rebirth though, being played while Kaworu begins he decent into Terminal Dogma.
When it comes to music, you can’t beat Anime Movies….