For those interested here's the now 9 year old alternate AFI list from Jonathan Rosenbaum.

ROSENBAUM'S ALTERNATE 100

Ace in the Hole/The Big Carnival (1951)

An Affair to Remember (1957)

Anatomy of a Murder (1959)

Avanti! (1972)

The Barefoot Contessa (1954)

The Big Sky (1952)

Bigger Than Life (1956)

The Black Cat (1934)

Bride of Frankenstein (1935)

Broken Blossoms (1919)

Cat People (1942)

Christmas in July (1940)

Confessions of an Opium Eater (1962)

The Crowd (1928) 

Dead Man (1995)

Do the Right Thing (1989)

The Docks of New York (1928) 

Eadweard Muybridge, Zoopraxographer (1974)

11 x 14 (1976)

Eraserhead (1978) 

Foolish Wives (1922)

Force of Evil (1948) 

Freaks (1932)

The General (1927)

Gentlemen Prefer Blondes (1953)

Gilda (1946)

The Great Garrick (1937)

Greed (1925)

Hallelujah, I'm a Bum (1933)

The Heartbreak Kid (1972)

Housekeeping (1987)

The Hustler (1961)

Intolerance (1916)

Johnny Guitar (1954)

Judge Priest (1934)

Killer of Sheep (1978) 

The Killing (1956)

The Killing of a Chinese Bookie (1976)

Kiss Me Deadly (1955)

The Ladies' Man (1961)

The Lady From Shanghai (1948) 

Last Chants for a Slow Dance (1977)

Laughter (1930)

Letter From an Unknown Woman (1948) 

Lonesome (1929)

Love Me Tonight (1932)

Love Streams (1984)

The Magnificent Ambersons (1942)

Make Way for Tomorrow (1937)

The Man Who Shot Liberty Valance (1962)

Man's Castle (1933)

McCabe & Mrs. Miller (1971)

Meet Me in St. Louis (1944)

Mikey and Nicky (1976)

Monsieur Verdoux (1947)

My Son John (1952)

The Naked Spur (1953)

Nanook of the North (1922)

The Night of the Hunter (1955)

The Nutty Professor (1963)

The Palm Beach Story (1942)

Panic in the Streets (1950)

Park Row (1952)

The Phenix City Story (1955)

Point Blank (1967)

Real Life (1979)

Reminiscences of a Journey to Lithuania (1971)

Rio Bravo (1959)

Scarface (1932)

The Scarlet Empress (1934)

Scarlet Street (1945)

Scenes From Under Childhood (1970)

The Scenic Route (1978) 

The Seventh Victim (1943)

Shadows (1960)

Sherlock Jr. (1924)

The Shooting (1967)

The Shop Around the Corner (1940)

The Sound of Fury/Try and Get Me! (1950)

Stars in My Crown (1950)

The Steel Helmet (1951)

Stranger Than Paradise (1984)

The Strawberry Blonde (1941)

Sunrise (1927)

Sylvia Scarlett (1935)

The Tarnished Angels (1958) 

That's Entertainment! III (1994)

This Land Is Mine (1943)

Thunderbolt (1929)

To Sleep With Anger (1990)

Tom, Tom, the Piper's Son (1969)

Track of the Cat (1954)

Trouble in Paradise (1932)

Vinyl (1965)

Wanda (1971)

While the City Sleeps (1956)

Will Success Spoil Rock Hunter? (1957)

Woodstock (1970)

The Wrong Man (1957)

Zabriskie Point (1970)