Baroque:

Diderik Buxtehude: Div. koralworks, preludes

Nikolaus Bruhns: "Nun komm der heiden Heiland"

Heinrich Scheidemann: "In dich hab' ich gehoffet, Herr"

J.S. Bach: Div. preludes & fuges, Toccatas, Passacaglia in c-minor, 
Fantasi i c-minor, korales and Concerti.

Antonio Vivaldi: Concerto in a-minor (transkr. for organ by J.S. Bach)

Nicolas de Grigny: Messe pour le paroisses

Classical:

Ludwig van Beethoven: All pieces for "flötenuhr"

Romanticism:

César Franck: All pieces

Louis Vierne: Symfoni nr. 3 and Suites.

Joseph Jongen: Petit prélude

Henry Mulet: Esquises Byantines

Augustin Barié: Trois piéces

Alexandre Guilmant: Div. pieces

Felix Mendelssohn: Div. sonatas

Max Reger: Benedictus

J.P.E. Hartmann: Sonata in g-minor and Fantasy in f-minor

Niels W. Gade: "Tonestykker" and chorales

Rued Langgaard: "Öde gader" and concert pieces

20th century and temporary:

Jehan Alain: Litanies a.o.

Maurice Duruflé: Requiem (for choir & organ)

Jean Langlais: Trois Paraphrases Gregorienes, Suite Breve, 9 piéces.

Olivier Messiaen: Livre du Saint Sacrement and La Nativité

Einar Trærup Sark: Toccata Primi Toni