From what I've seen and loved (excluding USSR):

1. "Daisies" (Vera Chytilova / Czechoslovakia / 1968) 
2. Few of Us (Sarunas Bartas / Lithuania / 1996)
3. Underground (Emir Kusturica / Federal Republic of Yugoslavia / 1995)
4. "The Turning Point" (Frank Beyer / East Germany / 1983)
5. "A bite to eat" and "Diamonds of the night" - one really should watch these two together! (Jan Nemec / Czechoslovakia / 1960 + 1964)
6. "Red Wheat" (Zivojin Pavlovic / Yugoslavia / 1971)
7. "Dimensions of Dialogue" (Jan Svankmajer / Czechoslovakia / 1982)
8. "The Red and the White" (Miklos Jansco / Hungary / 1967)
9. "Identification Marks: None" (Jerzy Skolimowski / Poland / 1964)
10. "Adoption" (Marta Meszaros / Hungary / 1975)
11. "Dancing in the Rain" (Bostjan Hladnik / Yugoslavia / 1961) 
12. "The Girl" (Marta Meszaros / Hungary / 1968) 
13. "The Little Mermaid" (Karel Kachyna / Czechoslovakia / 1975)
14. "When father was away on business" (Emir Kusturica / Yugoslavia / 1985)
15. "Sergeant Jim" (France Stiglic / Yugoslavia / 1955)
16. "The Lease" (Kristijonas Vildziunas / Lithuania / 2002)
17. "Normal People" (Oleg Novkovic / Federal Republic of Yugoslavia / 2001)
18. "Black Peter" (Milos Forman / Czechoslovakia / 1964)

and I also liked very much:

"Audition" (Milos Forman / Czechoslovakia / 1963)
"Do you remember Dolly Bell?" (Emir Kusturica / Yugoslavia / 1981)
"A short film about killing" (Krzysztof Kieslowski / Poland / 1988) 
"Time of the gypsies" (Emir Kusturica / Yugoslavia / 1988) 
"Innocence Unprotected" (Dusan Makavejev / Yugoslavia / 1968) 
Upir z feratu (Juraj Herz / Czechoslovakia / 1981)
"Dark Blue World" (Jan Sverak / Czech Repuvlic / 2001)
"The Ride" (Jan Sverak / Czech Republic / 1994)
"A quiet week at the house" (Jan Svankmajer / Czechoslovakia / 1969)
Rdeci boogie ali Kaj ti je deklica (Karpo Acimovic Godina / Yugoslavia / 1982)
"The Flat" (Jan Svankmajer / Czechoslovakia / 1968) 
"Faust" (Jan Svankmajer / Czech Republic / 1994)
"Ashes and Diamonds" (Andrzej Wajda / Poland / 1958) 
Spokoj "The Peace" (Krzysztof Kieslowski / Poland / 1976)
"Hands Up!" (Jerzy Skolimowski / Poland / 1981)
"Closely observed trains" (Jiri Menzel / Czechoslovakia / 1966)
"Knife in the water" (Roman Polanski / Poland / 1962)
"Czech Dream" (Vit Klusak, Filip Remunda / Czech Republic / 2004)
"Hi Tessa!" (Robert Glinski / Poland / 2001)
"Naked among wolves" (Frank Beyer / East Germany / 1963)

Probably forgot some, but still much to see!