There is essential, ongoing coverage and extensive background available at the Clarion Ledger's Neshoba County slayings archive. Of special recent note are some excerpts released just this past Sunday from the famous, secret interview with Klansman Sam Bowers, which contributed to the reopening of the case and the indictment of Edgar Ray Killen. It was Bowers who ordered the the slayings of Chaney, Schwerner and Goodman.
The Jackson Free Press has set up a separate Mississippi v. Edgar Ray Killen blog, with Donna Ladd, editor of the JFP and Neshoba County native, and Natalie Irby, a native of Jackson, MS, reporting. Under Ladd's editorship the JFP has become a model for how independent weeklies can incorporate blogging into their online format.
I also recommend the Jackson Free Press Chaney, Goodman & Schwerner Archive, which contains articles by Ladd, dating back to 2002. Ladd is a gifted writer, with a strong moral compass. See, for example, For The Children, Keep Your Eyes On The Prize, and 'Say These Words With Me.'