"...And you helped your landlady take out her garbage."

Neo dodging the bullets in swlo-mo anyone??

Interesting question! Hmm...Trinity lying on the floor muttering, "Get up, Trinity! Get UP!" . I understand how paralyzed she feels by the need to focus on that window, but must overcome the instinct and get going.
Second place: the blind guardian in the lobby.
Third: Neo looking up before the final shot of the movie.

The lobby scene
youtu.be/iuslUzbJEaw?t=1m24s

So many classic scenes! But I gotta go with the most classic of all; the opening scene of the first movie, with Trinity doing the first freeze-and-spin kick. 

Probably a bit lame but I do like the scenes between Neo and the Oracle. Otherwise all the action scenes were too good to play favourites.

Keanu Reeves saying "I know kung fu."

The scene on the Security Checkout.

Helicopter crash