Have you read the explanation and disclaimer?
Compared to the abundance on other topics, fourteeb on the battle of Gettysburg alone, there's not that much on Reconstruction.
Total links: 27
Value-added links: 6 (or 5.5: you'll see what I mean)
Civil War II: 1865-1965 - idiosyncratic account and interpretation from the Grazian Archive. Check out the welcome page and think carefully about the nature of this source and the needs of your research. If you have some knowledge of Reconstruction (actually the whole sweep of race relations between Appomattox and the Voting Rights Act of 1965), this might be fun--and perhaps even a useful challenge to your thinking. If you have little prior background, best to avoid. You have been warned.
Civil War Reconstruction and Recovery in Brazoria County, TX Rock on! Funded in part by a grant from Humanities Texas (formerly the Texas Council for the Humanities), this is graphics rich, vivid, and thought-provoking. Note to high school students and undergrads: Brazoria County, TX, is not the South as a whole. This is a close-up of this period as it took place in one small area. The text of this exhibit was written by Dr. Betsy Powers and relies heavily on her doctoral dissertation, From Cotton Fields to Oil Fields: Economic Development in a New South Community, 1860-1920 (University of Houston: 1994.)
"Reconstructing America: Consolidation of State Power 1865-1890" by Thomas J. DiLorenzo. DiLorenzo, a professor economics at Loyola College in Maryland, is a controversial historian and this essay (in pdf) offers a controversial interpretation of the period. All historical interpretations reflect to one degree or another the worldview of the interpreter. DiLorenzo identifies explicitly with the worldview exemplified in Rockwell.com. If you want to be challenged and/or provoked, check it out.
Reconstruction!!! - a chapter from Confederate Military History supplied by Shotgun's Home of the American Civil War page. For most purposes it's badly out of date and tedious to read. And as Shotgun notes: "WARNING! This is not what you were taught in school. It has a definite Southern bias. It is not politically correct! Nor should it be. It was written shortly after the war by Southerners about Southerners."
Reconstruction and Its Aftermath, 1865-1877 - This page simply introduces America's Reonstruction: People and Politics After the Civil War, which is where you may as well begin. This online exhibit is based on a traveling exhibition, originally sponsored by the Valentine Museum in Richmond. It opened in 1996 at the Virginia Historical Society and was subsequently shown at the South Carolina State Museum, Schomburg Center for Research in Black Culture, Museum of Florida History, Museum of the New South, and the Chicago Historical Society, where its tour ended in 1999. The development of this online exhibit was sponsored by the Gilder Lehrman Institute of American History.
Thin Gray Line: Confederate Veterans in the New South - Doesn't really fit in the Reconstruction section, but this is a good, "popular history" article from the Veterans of Foreign Wars.