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.
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.