The first novel that comes to mind is Gabriel Garcia Marquez’s One Hundred Years of Solitude. The other novels are again of Marquez; Love in the time of Cholera, No one writes to the Colonel, The Autumn of the Patriarch, Chronicle of a death foretold. Umberto Eco’s The Name of the Rose and Foucault’s Pendulum have to be somewhere there although they can be read as metaphysical thrillers or mysteries also. Midnight’s Children by Salman Rushdie and Beloved by Toni Morrison are there too . Gunther Grass’s Tin Drum is another great example though strictly not of that genre.
Werner Herzog”s Aguirre the wrath of God, and the Japanese films; Ugetsu, Woman of the Dunes and Rashomon have elements of magical realism. Tamil film Agraharattil Kazhuluthai is another example.