This is really tough, and of course youtube doesn't cater 100% to my eclectic tastes.
I've done top movies and top directors and such but top scene is really a tough one. So I started to make a list:
Apocalypse Now - Ride of the Valkyries or Death of Kurtz
The Matrix - Agent Smith and Morpheus
Apollo 13 - Launch Sequence or Steely Eyes Missile Man
Dr. Strangelove - Major Kon or Bodily fluids or Finale
2001 - Monolith Finale or First Transition (Blue Danube Waltz)
The Prestige - Consider the cost or best trick
American Beauty - Any Other Name
Blade Runner - Enhance or Blush Response or opening or Tears in Rain
The Maltese Falcon - Dreams are made of
Casablanca - Usual Suspects
Metropolis - Opening
Great Dictator - Finale
Thin Red Line - Finale
Saving Private Ryan - Dog Green Sector
Jurassic Park - T-Rex intro
Chinatown - Goldfish
Paths of Glory - Finale
Ghost In The Shell - Opening
Gladiator - They Say No or Honour Him
Top Gun - Finale or Death of Goose or That Loving Feeling
Titanic - Dance or Never Let Go
Derzu Uzala - The Wheat or Finale
Admiral - Kolchak becomes Czar
Alexander Nevsky - Grand Master intro
Battleship Potempkin - Stairs
Fifth Element - Heat
Men in Black - Finale
American Psycho - Business Cars
We live - This is your god
Escape from New York - Fuck the President
Wild Wild West - Grant and Lovelace
X-men - Magneto and the Police
Clockwork Orange - William Tell Overture or Luteveko Device
Fish Called Wanda - Apology
Twelve Monkeys - Fucking Crazy Dentist or Finale
The Fountain - Xibalba (Finale/Death is the Road to Awe)
Jarhead - Albert Camus / Sizzle Dick motherfucker
Boondock Saints - William Dafoe Intro
Lord of the Rings, Fellowship of the Ring - Moria sequence / Balrog or Death of Boromir.
Equilibrium - Beethoven's Sixth
Pulp Fiction - Dead idiot Storage or Finale
Raiders of the Lost Ark - Top Men or First Escape
Ghost Busters - I collect spores molds and fungus / Finale
Groundhog Day - Deathride of the Groundhog
Three Kings - Iraqi Ass Map or Saddam is Coming
Bottle Rocket - They'll never Catch Me
Rushmore - Finale (Wish I knew what I know now)
Lost in Translation - Roger moore / Rat Pack / Sentori Times or Alone in Kyoto
Risky Business - Love on a Train
Citizen Kane - Intro (News on the March)
Alien - Ash is an Android
Barry Lyndon - British Grenadiers or Lady Lyndon or Finale
Get Shorty - Intro or Green Onions
Heat - Finale or Robbery
Last of the Mohicans - Finale
Beyond the Black Rainbow - The Devil's blade
Koyanasqati - Finale
Mulan - Shan Yu (What do You see) or (Tell your Emperor)
Lion King - He Lives in You
Star Wars Episode Four - I find your Lack of Faith disturbing
Star Wars Episode Five - I am your Father
Star Wars Episode Six - Battle of Endor (Space sequence)
Shakespeare In Love - I am Faustus
Primer - What happens to engineers when they turn forty
Office Space - Damn it feels good to be a gangstar
Henry V - band of Brothers
Third Man - Cuckoo Clocks or Sewers
Kingdom of Heaven - Burning the Past
Hunt For Red October - Intro
Of which, top Three:
1) [youtube]
http://www.youtube.com/watch?v=5IvPIWzQcUY[/youtube]
2) [youtube]
http://www.youtube.com/watch?v=a_saUN4j7Gw[/youtube]
3) [youtube]
http://www.youtube.com/watch?v=wxrWz9XVvls[/youtube]
Alternative:
4) [youtube]
http://www.youtube.com/watch?v=pJH8hO7VlWE[/youtube]
5) [youtube]
http://www.youtube.com/watch?v=UOi6v5DD_1M[/youtube]
6) [youtube]
http://www.youtube.com/watch?v=xGTe1vF679U[/youtube]
Bonuses:
[youtube]
http://www.youtube.com/watch?v=7xfb5vYxYk4[/youtube]
[youtube]
http://www.youtube.com/watch?v=j0pWNprikrk[/youtube]
[youtube]
http://www.youtube.com/watch?v=gjPGmSqadxM[/youtube]