Fuck me this is gonna be a long list if I throw out everything.
If you want "less than mainstream but still known," Sigur Ros, Mogwai, This Will Destroy You, Funeral, The Church, or Officium Triste depending on the day and mood.
Somewhere in between that level of notoriety and the next one down is Mouth of the Architect.
If you want "pretty unheard of," Sunn O))), Boris, Stars of the Lid, Tenhi, and Labradford, see note above.
If you want "really underground," Thergothon (unless you ask funeral doom fans, they're generally unknown to my knowledge), Aedra, Buried at Sea, Indian Jewelry (by the way, I'm from and going to college in Houston, where these guys are from. yay!) and Black Shape of Nexus.
If you want "no one knows who this is," Bull of Heaven, Until Death Overtakes Me, Wiljen Wij, Chuter, and Atlanticore.
I have a hard time deciding between those; Mouth of the Architect, Sigur Ros, This Will Destroy You, Mogwai, Boris, and Stars of the Lid are frequent answers to "my favorite band," though.