Here are the best free tools that I know of for exploring black family history.
The National Archives African-American Research page is important to note, even though very few of their records are actually online (come on, NARA...what's taking so long?). Still, their holdings from the Freedmen's Bureau, military records, and slave trade files are essential records for African-American history and family research.
George Washington Williams, author, legislator, jurist
A list of large slaveholders in the South, and African American surnames has been compiled for the period 1860-1870. It's a bit cumbersome to use, but a good resource just the same.
A small but notable list: 1790 Census: Slave Holders, Other Free Persons and Slaves - Cheshire County - New Hampshire
Afrigeneas is probably the best source of overall information on African American genealogy. There are several good name lookup indexes at the site under the Records heading, including Census, Deaths, Slaves, and a growing Surnames database.
The Harlem Hellfighters were the first black regiment to fight in World War I, and their muster records are online. You can read more about the collection.
Alabama State Archives also has military records online in their WWI Gold Star database...enter African in the Race field to pull up African American records. These are occasionally amazing file, with photos, full biographies, family history, and more.
There is also the Alabama Archives database of 1867 Voter Registrations, which also includes race information. This is a pretty sizable collection, and well worth a visit.
A very nice blog of one black family's history.
An online ebook, History of the Negro Race in America From 1619 to 1880 Vol 1. Written in 1885 by George Washington Williams, "first colored member of the Ohio legislature..." Vol II is online as well.
North American Slave Narratives. Several hundred written records from the Digital Library of Georgia.
The Digital Library on American Slavery at UNC is a pretty new, hopefully growing resource that looks to have some excellent materials online, chiefly from petitions to state legislatures and county courts regarding slaves. These records are fully searchable.
There are a number of historical black newspapers that can be searched online, and at no cost.
I covered some additional resources on African American family history in two earlier posts on Slave Records, and on Michelle Obama's Family Tree, so be sure to visit them as well.
Visit the main page of Free Genealogy Tools for more, umm, free genealogical tools.
And don't forget to also check for African-American family history at Ancestry.com and NewspaperArchive.com. These are subscription databases, but they are among the most powerful research tools available for looking into family roots.