The Civil War. War Between the States. War of Northern Agression. The Southern Rebellion. War for Southern Independence.
Whatever you call it, this was one of the great conflicts in history. It was also the beginning of modern military record-keeping, so that there are deep family history resources available from this era, regardless of whether your ancestors wore Blue or Gray. Some mid-19th century resources that you should be aware of include:
The Civil War Soldiers and Sailors System (CWSS), which I wrote up in an earlier blog post.
Civil War Soldiers of the Sixth Maine Infantry
The Making of America collection (a joint project of Cornell University, and the University of Michigan) has a number of important collections from the Civil War era that are useful for family history. The War of the Rebellion reports are comprehensive records of the Union and Confederate actions, including prisoners, correspondence, field actions, etc. Note than many first names tend to be abbreviated (eg Danl for Daniel). Civil War Naval Records also are a deep resource.
Cornell also houses an important Anti-Slavery collection. The materials here can be especially useful in researching African-American family history.
You can view, or download, the official List of pensioners on the roll January 1, 1883: giving the names of each pensioner, the cause for which pensioned, the post-office address, the rate of pension per month, and the date of original allowance (whew!). These records can be easily searched for your family names; just use the "Search in this book" feature on the left hand side of the page when you visit the above link. This is only one of several volumes; see the "Other editions" links at Google Books for additional volumes in this series.
Also from Google Books, here's a listing of fully-searchable Directories from the Civil War era. Think of them as phone books for the days before the phone was invented! There are directories here for Boston, Rochester, Hartford, Madison, Doniphan County (Kansas), and many other places. There's even a directory of clergymen.
And take a look at the Special Collections page of Free Newspaper Archives, where you'll find several archives focused on the Civil War from both a North and South perspective.
Visit the main page of Free Genealogical Tools for more, umm, free genealogical tools.
And don't forget to also check for your 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.