Mari's comment about the 12th angel, near the end of 3.33: "Besides, after defeating the last angel we don't know what kind of evil could appear. Are you not worried?". It's hilarious on a meta level, given how ridiculously elaborated the apocaypses can get in this franchise.
Some translations make her say "Besides, I'm curious to see what will happen once the final Angel is destroyed.", which makes the scene less funny and more ominous.
The last line of the trailer for 2.0: "Oh, and lots of fanservice!"
The shell casings of the chaingun that Unit-01 uses on the fifth angel raining down on and crushing a car was somehow very funny when looked on from a More Dakka perspective.
The kids decide to head to the aquarium (conveniently shaped like the Tree of Life). Since Second Impact, a massive red tide has poisoned all of Earth's oceans, so the aquarium has very strict measures about sanitation. Everyone basically has to go through a hyper washing machine, getting tossed around and scrubbed raw.
Unit 02 does a highly-complicated acrobatic maneuver, lands feet-first, and sends Misato's car flying arse over tit in the process. While Misato and Shinji are still inside.
And the car gets stopped by Unit 00's foot.
You will not be able to take Sahaquiel seriously if you have seen the "Double Rainbow" version of it on Youtube prior to watching the real version.
A bit off narm here, but the name Wille (pronounced Will-y) can be stupidly hysterical if it catches you off guard. It doesn't help that under the logo, there's a big white paint splotch to go with it.
Toji being chased by Pen-Pen when he takes Rei's (unwanted) meal.