Working with a small independent publisher allows the author more creative control over his/her book. Small publishers tend to work more intimately with their authors, including them in many of the decisions. Also, a small publishing house may be more willing to take a risk on non-commercial work as long as the writing meets their standards.
I've had the satisfying experience of working with White Bird Publishing http://whitebirdpublications.com/ since its beginning days. Over the years, I've developed a personal relationship with key people in the company. Their acceptance standards are high and every book accepted for publication goes through a rigid process.
I am kept informed of my manuscript's process every step of the way. Even though I am one of their multi-published authors, I still have to give final approval each step of the way, say in the formatting, cover design, and proofing. Only when I give my approval does the process go forward. I really appreciate being closely involved in the publication process.
So. if you're considering using a small press, be sure to do your homework. Check out their website, look over what they publish, contact their published authors and ask questions. Science Fiction and Fantasy Writers of America, Inc.'s article on the subject (http://www.sfwa.org/other-resources/for-authors/writer-beware/small/) will get you started.
Listed below are some other resources to get you started in the right direction.
Publishers Marketing Association (http://pma.com.pk/) is a trade association of independent publishers organized to advance the professional interest of independent publishers.
Small Press United (http://smallpressunited.com/) seeks to draw awareness to and provide information about small presses. It sponsors an annual book fair, holds regular workshops, and features readings by small press authors.
Small Press Association of North Amrica (www.spannet.org) forms a strategic alliance among small publishers and independent booksellers. It helps to create entrepreneurial opportunities for new small publishers.