The Avalon Project is a great resource for primary source documents from US History that has previously been featured on Free Technology for Teachers. Recently I started exploring another good source of primary source documents hosted by the National Humanities Center. The National Humanities Center Toolbox Library host eight collections of primary source documents and images. The collections are categorized by eras in US History. Each document and image in the collections is accompanied by discussion questions and or a reading guide.

Applications for Education
There are many primary source document books that can be purchased. Most of those are simply filled with documents that are in the public domain. Online resources like the National Humanities Center Toolbox Library and The Avalon Project contain much of the same material is available at no cost to schools (other than perhaps the cost of printing copies for a classroom).

Here are some related items that may be of interest to you:
National Archives Our Documents Source Book
Documenting the American South