AfriGeneas 
http://www.afrigeneas.com/
 
The oldest and largest African American genealogy site. If you are researching African Ancestry, "all roads lead to AfriGeneas." Fresh content daily. Searchable.

• 40,000 surnames

• 5,000 obituaries and death records

• 4,000 slave records

• 8 years of AfriGeneas list archives with contributions from some of the best known researchers in the field. 

• Networking and collaboration tools: message boards; mail lists; chats; calendars
   

African-Native American Genealogy
http://www.african-nativeamerican.com/
 
Angela Walton Raji's companion website for researching the African citizens of the Cherokee, Choctaw, Chickasaw, Creek and Seminole Nations. Frequently updated.

• Frontier Freedman's Journal index

• Freedmen surnames

• Dawes Roll Freedmen Citizens

• Negroes in the Creek and Seminole Nations

• Oklahoma Freedmen message board
   

Lest We Forget
http://www.coax.net/people/LWF/

Bennie McRae's comprehensive African American military site with online records and resources for researching the period from the Revolutionary War until the present. Frequently updated.

• Military records reference desk

• United States Colored Troops

• Military Research message board
   

Free African Americans of VA, NC, SC, MD and DE
http://www.freeafricanamericans.com/

Paul Heinegg's online text with histories of families who were free during the colonial period. Searchable. Frequently updated.
 

Afrolumens Project
http://www.afrolumens.org/

George Nagle's successor site to Slavery in Pennsylvania. 
 

African American Cemeteries Online
http://www.prairiebluff.com/aacemetery/

One-stop resource for searchable cemetery listings and pointers to offsite listings and other cemetery sites. Clearinghouse for preservation issues and alerts. Frequently updated.

• Hundreds of cemeteries listings with thousands of names

• Cemetery discussion and query board
   

African American Genealogical Society of Northern CA
http://www.aagsnc.org/

Excellent starting point. Regional as well as general resources. Frequently updated.

• Library 

• Databases
   

The African American Experience in Ohio
http://dbs.ohiohistory.org/africanam/

One of the earliest state sites and still one of the best. Chronicles the lives of Ohio's African Americans from 1850-1920. Part of "American Memory." Searchable and browseable. 
 

Database of Servitude and Emancipation Records
http://www.sos.state.il.us/departments/archives/servant.html

This is the online standard that every state archive should be measured against. Ongoing projects. Ease of use. Fully searchable across databases.
  

The Freedmen's Bureau Online
http://freedmensbureau.com/

Part of Christine Charity's pioneering genealogy site. Unique resource. Infrequently updated.
 

Afro-Louisiana History and Genealogy
http://www.ibiblio.org/laslave/introduction.php

Online version of Gwen Midlo Hall's Louisiana Slave databases. Over 100,000 names. Fully searchable.
 

Genealogy of Jamaica
http://www.rootsweb.com/~jamwgwl
 
If you have Jamaican roots then this is a must-visit site. 
 

Cyndi's List: African-American
http://www.cyndislist.com/african.htm

Cyndi Howell's regularly updated list of links to African American resources.