How about posting our alternative lists, or a list of films you would possibly include in your Top 100 which aren't mentioned in the AFI list?

Here goes my selection of possible contenders ( in chronological order):

Shoulder Arms (Charles Chaplin / 1918) 
Our Hospitality (Buster Keaton, John G. Blystone / 1923)
The Wind (Victor Sjstrm / 1928) 
A Woman of Affairs (Clarence Brown / 1928) 
Dishonored (Josef von Sternberg / 1931)
Frankenstein (James Whale / 1931)
Queen Christina (Rouben Mamoulien / 1933)
Design for Living (Ernst Lubitsch / 1933)
Now, Voyager (Irving Rapper / 1942)
To Be or Not to Be (Ernst Lubitsch / 1942)
Five Graves to Cairo (Billy Wilder / 1943)
Notorious (Alfred Hitchcock / 1946)
Monsieur Verdoux (Charles Chaplin / 1947)
Rope (Alfred Hitchcock / 1948) 
Limelight (Charles Chaplin / 1952)
Magnificent Obsession (Douglas Sirk / 1954)
Rebel without a Cause (Nicholas Ray / 1955) 
The Night of the Hunter (Charles Laughton / 1955)
East of Eden (Elia Kazan / 1955)
The Incredible Shrinking Man (Jack Arnold / 1957)
Paths of Glory (Stanley Kubrick / 1957)
Anatomy of a Murder (Otto Preminger / 1959)
Judgment at Nuremberg (Stanley Kramer / 1961)
Carnival of Souls (Herk Harvey / 1962)
The Birds (Alfred Hitchcock / 1963)
Salesman (Albert Maysles, David Maysles, Charlotte Zwerin / 1968) 
Five Easy Pieces (Bob Rafelson / 1970)
Zabriskie Point (Michelangelo Antonioni / 1970)
Fingers (James Toback / 1977)
The Elephant Man (David Lynch / 1980)
The Big Red One [reconstructed version] (Samuel Fuller / 1980)
Permanent Vacation (Jim Jarmusch / 1980)
Eyewitness (Peter Yates / 1981)
Pennies from Heaven (Herbert Ross / 1981)
Victor/Victoria (Blake Edwards / 1982)
Conan the Barbarian (John Milius / 1982)
Scarface (Brian De Palma / 1983)
Stranger than Paradise (Jim Jarmusch / 1983)
Blue Velvet (David Lynch / 1986)
The Unbearable Lightness of Being (Philip Kaufman / 1988) 
Batman (Tim Burton / 1989)
Back to the Future Part II (Robert Zemeckis / 1989)
Edward Scissorhands (Tim Burton / 1990)
Dances with Wolves (Kevin Costner / 1990)
Wild at Heart (David Lynch / 1990)
The Fisher King (Terry Gilliam / 1991)
Paris Trout (Stephen Gyllenhaal / 1991)
Of Mice and Men (Gary Sinise / 1992)
Basic Instinct (Paul Verhoeven / 1992)
King of the Hill (Steven Soderbergh / 1993)
Flesh and Bone (Steven Kloves / 1993)
Mad Dog and Glory (John McNaughton / 1993)
Fearless (Peter Weir / 1993)
A Perfect World (Kevin Costner / 1993)
Arizona Dream (Emir Kusturica / 1993)
Groundhog Day (Harold Ramis / 1993)
Maverick (Richard Donner / 1994)
The Addiction (Abel Ferrara / 1995)
Se7en (David Fincher / 1995)
Twelve Monkeys (Terry Gilliam / 1995)
Leaving Las Vegas (Mike Figgis / 1995)
Heat (Michael Mann / 1995)
Dead Man (Jim Jarmusch / 1995)
The Ice Storm (Ang Lee / 1997)
I Married a Strange Person! (Bill Plympton / 1997)
Lost Highway (David Lynch / 1997)
Gattaca (Andrew Niccol / 1997)
Pi (Darren Aronofsky / 1998) 
Rushmore (Wes Anderson / 1998) 
Dark City (Alex Proyas / 1998) 
The Big Lebowski (Joel and Ethan Coen / 1998) 
Celebrity (Woody Allen / 1998) 
City of Angels (Brad Silberling / 1998) 
Buffalo '66 (Vincent Gallo / 1998) 
The Thin Red Line (Terrence Malick / 1998) 
Magnolia (Paul Thomas Anderson / 1999)
Eyes Wide Shut (Stanley Kubrick / 1999)
Jesus' Son (Alison Maclean / 1999)
Sweet and Lowdown (Woody Allen / 1999)
Being John Malkovich (Spike Jonze / 1999)
Before Night Falls (Julian Schnabel / 2000)
Cast Away (Robert Zemeckis / 2000)
Unbreakable (M. Night Shyamalan / 2000)
Mulholland Dr. (David Lynch / 2001)
Monster's Ball (Marc Forster / 2001)
The Royal Tenenbaums (Wes Anderson / 2001)
The Hours (Stephen Daldry / 2002)
Punch-Drunk Love (Paul Thomas Anderson / 2002)
Adaptation. (Spike Jonze / 2002)
25th Hour (Spike Lee / 2002)
The Brown Bunny (Vincent Gallo / 2003)
21 Grams (Alejandro Gonzlez Irritu / 2003)
Before Sunset (Richard Linklater / 2004)
Birth (Jonathan Glazer / 2004)
The Life Aquatic with Steve Zissou (Wes Anderson / 2004)
Eternal Sunshine of the Spotless Mind (Michel Gondry / 2004)
The New World (Terrence Malick / 2005)