EPA's "Clean Water Act Section 401 Water Quality Certification: A Water Quality Protection Tool for States and Tribes" was released April 2010. This new handbook describes CWA §401 certification authorities, the way different state and tribal programs use certification, and how state and tribal certification programs leverage available resources to operate their certification programs. The handbook is available here.

ASWM Publications:

State 401 Certification Links
States and Tribal 401 Certification of Nationwide Permits (2012)
States 401 Certification of Nationwide Permits (2007)
Section 404 Nationwide Permit Resources for 401 Certification
401 Certification Resources