My favourites:

Closely Observed Trains (Menzel)
Marketa Lazarova (Vlacil)
The Hand (Trnka)
Daisies (Chytilova)
The Party and the Guests (Nemec)
Valerie and her Week of Wonders (Jires)
Alice (Svankmajer)
The Cremator (Herz)
The Ear (Kachyna)
A Blonde in Love (Forman)

i'm confident i'd add something by Karel Zeman when i can get to see some of his feature-length films in full...