I have recently bought a big fat compendium that lists about 140 of the most prolific manga artists. (http://www.taschen.com/pages/en/catalogue/books/design/all/facts/03822.htm)
I will list some of them that could be labeled "underground" or "independent" later when I have time.

I also believe there were some related posts on http://wakaba.c3.cx/soc/index.html but I cannot find them right now.