This list is complementary to the list of major church music publishers. Companies on this list are smaller, or perhaps more specialised or focussed on a particular geographic market rather than operating internationally. They are not necessarily lower-quality.
This is a work-in-progress - leave a comment below if your company would like to be added.
ABC Publishing (Anglican Book Centre) - publishers of Anglican resources in Canada
Alfred Music Publishing a US company that operates in several other countries (inc the UK and Australia). They are a music-education publisher, but have a large selection of sacred choral, and other, music.
Augsburg Fortress - the publishing house of the Evangelical Lutheran Church in America.
Bechenhorst Press -a privately owned US publishing copany, focussing on sacred music but not aligned with any particular denomination
Boosey & Hawkes: a world-wide classical music publisher, whose catalog includes sacred music intended for current liturgical use, including James McMillan's works.
CanticaNOVA Publications - an American company, who describe themselves as providing quality / traditional liturgical music for the contemporary Catholic Church.
Columba - an Irish publisher of "thoughtful books for a thinking church", producing titles for both Catholic and Church of Ireland audiences. They have released a small number of hymn books featuring Irish composers, which are available on their website..
Concordia - the official publisher of the Lutheran Church's Missouri Synod - USA.
Church House Publishing - the official publisher to the Archbishops' Council and the General Synod of the Church of England (UK)
Church Publishing Incorporated (CPI) - Based in New York City (USA). An official publisher for The Episcopal Church
Genesis Publications - Anglican resources for Australia and New Zealand
Good for the Soul Music - a US small company, mentioned as having some interesting settings of the ICEL-2008 Catholic Mass
ILP / International Liturgy Publications - a Nashville, Texas, US company publishing Catholic materials including a number of charismatic style composers.
Kingsfold Music - another small US company
Liturgical Press - founded by Saint John's Abbey (Order of Saint Benedict, Collegeville, MN, USA) in 1926. Produce a very wide range of liturgical and music materials, including some Spanish-language.
RSCM (Royal School of Church Music), a UK charity, originally English and choral, now international and supporting many genres - the make some of their income by publishing materials, which are available for purchase through their on-line store.
Small Choirs: A UK-based website which provides downloads of copyright-free church music (hymns, anthems etc) arranged for small choirs and choirs with few or no male singers. Also provides an annual festival/workshop in London, for singers from such choirs.
Spectrum Publications: an Australian company, publishing materials by local authors and composers, and providing a distribution channel for self-published materials.
St James Music Press - a US company. Materials purchased from them may be photocopied and reproduced in your church for no additional fees, and with no reporting required.
Taizé - French community of brothers, which publishes short meditative songs, to be used as rounds / chants. Official title: Ateliers et Presses de Taizé (A&PT)
United Methodist Publishing House - the official publishers for the United Methodist church in the US
Veritas - originally the Catholic Truth Socity of Ireland, it was later merged with a communications centre. Owned by the Catholic bishops in Ireland. A general purpose publisher for the Catholic church in Ireland. Produces various liturgy materials and sometimes publishes music. Brands include Lindisfarne Books, which is for the UK market.
Weston Priory - The Benedictine Monks of Weston Vermont
An order of monks who have produced folk-style music for some time - Gregory Norbett is the best known. They make their work available for purchase via their website. Some songbooks are available for purchase, and lead sheets for tracks on their most recent CD are available for free download.
White Light Publishing - an English company, featuring the work of David Ogden and others. Includes pieces for choral and congregational use.
Wild Goose Publications - publishing house of the Iona Community in Scotland. Materials from a Celtic background, but reflecting the current population and issues.
Willow Connection: An Australian company that both publishes for the educational and Christian markets, and represents a wide range of other music publishers in Australia. They also run As One Voice