While many of his compositions were for orchestra, organ, or chamber ensembles, he also wrote choral music. His large-scale Mass in D minor (1866) was first performed in Berlin, and later in the United States. The first recording was finally released in 1978, and a new critical edition of the score is reportedly in preparation. At least two performances of the Mass took place in 2012, and I was lucky enough to attend one of them. This YouTube video, of the final movement (Dona nobis pacem), is from the other one, at West Chester Universioty in Pennsylvania.
Paine also wrote a handful of hymn tunes. He served as one of the musical editors for Hymns and Songs of Praise for Public and Social Worship (1874) where most (if not all) of them appeared. Unfortunately no one has documented these tunes on any of the usual hymn websites, so no sound files are yet available.
Three Years Ago: John Knowles Paine