1967: Bonnie and Clyde.
1968: The Battle of Algiers.
1969: Z.
1970: Five Easy Pieces.
1971: The Last Picture Show.
1972: The Godfather.
1973: Cries and Whispers.
1974: Scenes from a Marriage.
1975: Nashville.
1976: Small Change.
1977: 3 Women.
1968: An Unmarried Woman.
1979: Apocalypse Now.
1980: The Black Stallion.
1981: My Dinner With Andre.
1982: Sophie's Choice.
1983: The Right Stuff.
1984: Amadeus.
1985: The Color Purple.
1986: Platoon.
1987: House of Games.
1988: Mississippi Burning.
1989: Do the Right Thing.
1990: GoodFellas.
1991: JFK.
1992: Malcolm X.
1993: Schindler's List.
1994: Hoop Dreams.
1995: Leaving Las Vegas.
1996: Fargo.
1997: Eve's Bayou.
1998: Dark City.
1999: Being John Malkovich.
2000: Almost Famous.
2001: Monster's Ball.
2002: Minority Report.
2003: Monster.
2004: Million Dollar Baby.
2005: Crash.
2006: Pan's Labyrinth.
2007: Juno.
NOTE: Roger Ebert chose to list his favorite films of 2008 and 2009 alphabetically.
Here's the list from 2008 and here's the list from 2009.