Shinji and Ghost-Asuka's conversation about Asuka (After the 16th Angel, and Asuka's mind loss), and how he refuses to abandon her, despite her doll-like state.
The picture at the top of the heartwarming fanfiction page, showing that despite everything, Shinji and Asuka have finally come to fully accept each other. Might border on Tear Jerker if you are part of the camp that believes that they are dead.
Or the fact that Shinji/Ghost-Shinji willing gave up his dream, so Ghost-Asuka wouldn't be alone.
Ghost-Asuka's converstation with God, and where that leads... and finally, from the final volume... well, actually, it is better expressed by video: here. Especially the last couple of minutes, when the soundtrack changes. You'll know the part I'm talking about. Pity the video creator had to write such an overblown introduction, but otherwise, meh.
Shinji and Asuka coming to accept each other in the first issue (with the added eye candy of them having sex), and again in the final issue.