These are a few of my favorite scenes... 
(the yellow descriptions are links...)

Good Will Hunting - "I have to go see about a girl"

The Virgin Suicides - Makeout scene

Let the Right One In - Rubiks cube

Moulin Rouge! - Le Tango De Roxanne 

Amelie - Blind man

 

There Will Be Blood - "I drink your milkshake"

Rushmore - This guy ~~ best chapel speaker I have ever seen.

Eternal Sunshine of the Spotless Mind - "This is it joel. It's gonna be gone soon."

Garden State - Completely original moment in human history

Magnolia - Coincidence 

Kill Bill - Escape

The Sandlot - "One day it became too much for Michael Squints Palledorous"

The Good the Bad and the Ugly - Final showdown