His compositions include five symphonies, concertos for violin and for organ, six string quartets, numerous solos and duos for strings and winds with and without piano of which several have been recorded (an oboe sonata is on CD). Raphael also composed organ, piano and choral works. He was also responsible for arranging a performance version of Antonín Dvořák's Cello Concerto in A major (1865) when its piano and cello score was discovered in 1918.
He was also an editor of classical and baroque scores for Breitkopf and Härtel, preparing editions of, for example, flute sonatas by Frederick the Great and works by Vivaldi and Johann Sebastian Bach (some of these can be found in the Cornell University Library).