Below is my list (not a complete listing by any means) of small and/or independent publishing houses that have a Christian fiction imprint, or that are Christian fiction friendly/family friendly.
Splashdown: Christian sci-fi, fantasy http://www.splashdownbooks.com
Stonehouse Ink: edgy Christian fic http://www.thestonepublishinghouse.com/
Sword of the Spirit: Christian fiction, womens fic, romance, YA. http://donaldjamesparker.com/ProductDetails.aspx?id=419
Treble Heart Books: Contemporary, Paranormal, Romantic Suspense, Historical. http://www.trebleheartbooks.com/
Written World Communications: Imprints are Harpstring and Patchwork
Mixed: (Family Friendly, Christian Friendly)
Black Lyon Publishing: literary romance, historical romance contemporary romance, Christian
Muse It Up Publishing: Canadian ebook publisher. All genres. Will accept submission of gen market stories with one or more Christian characters that are not Inspy stories per se.
Samhain: romance, mystery-suspense, action-adventure
Port Yonder Press: Christian titles and general market. http://portyonderpress.com/home.aspx