I'm a bit in a list-mood, so here are my selections: 

1960s 

La Jetée "The Pier" (Chris Marker / France / 1962) 
Le Mépris "Contempt" (Jean-Luc Godard / France / 1963) 
Suna no onna "Woman in the Dunes" (Hiroshi Teshigahara / Japan / 1964)
Deus E o Diabo na Terra do Sol "Black God, White Devil" (Glauber Rocha / Brazil / 1964) 
Andrei Rublyov "Andrei Rublev" (Andrei Tarkovski / Soviet Union / 1966) 
Bonnie and Clyde (Arthur Penn / USA / 1967) 
Csillagosok, katonak "The Red and The White" (Miklos Jancso / Hungary, Soviet Union / 1967) 
2001: A Space Odyssey (Stanley Kubrick / USA, UK / 1968) 
Goto, l'île d'amour "Goto, Island of Love" (Walerian Borowczyck / France / 1968) 
Sayat Nova "The Color of Pomgranates" (Sergej Paradjanov / Soviet Union / 1968) 

1970s 

Iko shashvi mgalobeli "Lived Once a Song-Thrush" (Otar Iosseliani / Soviet Union / 1970) 
Tokyo senso sengo hiwa "The Man Who Left His Will on Film" (Nagisa Oshima / Japan / 1970) 
Zabriskie Point (Michelangelo Antonioni / USA / 1970) 
La maman et la putain "The Mother and the %%%$$" (Jean Eustache / France / 1973) 
Mes petites amoureuses (Jean Eustache / France / 1974) 
Barry Lyndon (Stanley Kubrick / UK / 1975) 
Dzieje grzechu "Story of a Sin" (Walerian Borowczyk / Poland / 1975) 
Örökbefogadás "Adoption" (Márta Mészáros / Hungary / 1975) 
1900 (Bernardo Bertolucci / Italy, France, West Germany / 1976) 
Suspiria (Dario Argento / Italy / 1977) 

1980s 

Possession (Andrzej Zulawski / France, West Germany / 1981) 
Moonlighting (Jerzy Skolimowski / UK / 1982) 
Sans soleil "Sunless" (Chris Marker / France / 1982) 
Klassenverhältnisse "Class Relations" (Danièle Huillet, Jean-Marie Straub / West Germany, France / 1984) 
La pirate "The Pirate" (Jacques Doillon / France / 1984) 
Tenshi no tamago "Angel's Egg" (Mamoru Oshii / Japan / 1985) 
Ran (Akira Kurosawa / Japan, France / 1985) 
Offret "The Sacrifice" (Andrei Tarkovsky / Sweden, UK, France / 1986) 
Hotaru no haka "Grave of the Fireflies" (Isao Takahata / Japan / 1988) 
Majo no takkyûbin "Kiki's Delivery Service" (Hayao Miyazaki / Japan / 1989) 

1990s 

Nema-ye Nazdik "Close Up" (Abbas Kiarostami / Iran / 1990) 
Trys dienos "Three Days" (Sharunas Bartas / Soviet Union / 1991) 
Groundhog Day (Harold Ramis / USA / 1993) 
Tikhiye stranitsy "Whispering Pages" (Alexander Sokurov / Russia, Germany / 1993) 
Haonan haonu "Good Men, Good Women" (Hsiao-hsien Hou / Taiwan, Japan / 1995) 
Heat (Michael Mann / USA / 1995) 
Moe no Suzaku "Suzaku" (Naomi Kawase / Japan / 1996) 
The Thin Red Line (Terrence Malick / USA, Canada / 1998) 
Wandâfuru raifu "After Life" (Hirokazu Koreeda / Japan / 1998) 
Pola X (Les Carax / France, Switzerland, Germany, Japan / 1999) 

2000s 

Eureka (Shinji Aoyama / Japan / 2000) 
Zhantai "Platform" (Zhang Ke Jia / China, Hong Kong, Japan, France / 2000) 
Bungalow (Ulrich Köhler / Germany / 2002) 
Kôfuku no kane "Blessing Bell" (Sabu / Japan / 2002) 
The Brown Bunny (Vincent Gallo / USA, Japan, France / 2003) 
Marseille (Angela Schanelec / Germany / 2004) 
Sud pralad "Tropical Malady" (Apichatpong Weerasethakul / Thailand, France, Germany, Italy / 2004) 
Au-delà de la haine "Beyond Hatred" (Olivier Meyrou / France / 2005) 
Batalla en el cielo "Battle in Heaven" (Carlos Reygadas / Mexico, Belgium France, Germany / 2005) 
couldn't decide for a no.10 - too many contenders...