This acappella version of Cruel Angel's Thesis is absolutely beautiful and haunting; had it played during some of the more emotional moments later on, it could have enhanced the impact, which is saying a lot.
"Komm, sŁsser Tod", dudes. Not only is it catchy as hell and surprisingly touching, the dichotomy of the pleasant tune and painful lyrics gives it an ambiguity that makes it a perfect match for the scene it plays in.
The version of "Fly Me to the Moon" that plays after Kaworu's death in Episode 24 stands out from the rest because it's the only ending to not have any singing, whereas the rest are all sung by different people.
"Rei I" is a really chilling and beautiful piano piece.
"Rei III" puts the same melody to a fusion of orchestra and hard rock, making for a powerful mix.
"Jesus Bleibet Meine Freude", because of the moment in End that it highlighted: the moment after Shinji kills the human race, he comes to realize that the reality he's been living in is one that he alone created for himself.
Five more songs to add to the pile: "Beautiful World", the song sung by Utada Hikaru for the movies, available in both Standard (Movie 1) and Remixed (Movie 2) editions, the new song by Utada Hikaru, "Sakura Nagashi" (Movie 3), Destiny, which is played during the race to catch Sahaquiel, and Fate, which plays during the battle against Sahaquiel.
Also from Rebuild 2.0, there's "In My Spirit". If there's any song that says that the entire human race is completely, utterly, and absolutely screwed, it is this song.
3.0 has an utterly awesome piece called "God's Message" that plays during the six minute preview. It's also a remix of Shirō Sagisu's earlier piece from Nadia: The Secret of Blue Water titled "Light of Babel.
Another Nadia remix is the Wunder's jaw-droppingly awesome theme, The Anthem.