Eye Scream: When Asherah ripped out one of Unit 01's eyes, Shinji's synch rate was high enough to experience some of the pain (although not enough for any physical injury).
Has Two Mommies: Shinji was raised by two women (a FSB agent and an Ashcroft sorceress) selected by his father.
I Don't Know Mortal Kombat: A non-video game variant, where Shinji's skills are strictly attuned to being in the Eva, so he can do nothing but be a punching bag for Toja while in school. His gun training does transfer to the Light Gun Arcade game, but those are designed for scouting potential military recruits anyway.
Naked First Impression: When Shinji meets her for the "first" time, when she is naked in the medical tank and missing one eye. The real (maybe) first time is when she incinerates some hostile operatives Alma-style right before his eyes, which causes Shinji to feel very uneasy everytime he is near her.
Lethal Chef: She has the same sensory issues (and resulting culinary fallout) that she had in ANE. This time around, though, it's due to brain damage caused by exposure to the environment of Leng as opposed to ANE's more directly brutal reason. At least, that's what Ritsuko tells Shinji. It's only part of the truth, and the rest, from her inner dialogue, is best left unspoken.
Tuck and Cover: She did this to Shinji when the nuke was used against Asherah.