I came across this interesting website today. I haven't dug into it much but it looks like it would be of value to researchers. The quote below is from the main page and is written by noted scholar William C. Davis from Virginia Tech.
For many years the newspapers of the Civil War era were probably the most neglected of all sources, and yet they are one of the richest. The reason no doubt lay in the sheer mass of them, their inaccessibility, and the fact that they were not indexed. Few if any scholars had the time or resources to spend weeks and months scanning page by page in the hope of finding something of use to their projects. Yet the newspapers are the surest windows on the attitudes of the time, despite their inevitable editorial bias.
All of the daily affairs of the common people play out in the pages of newspapers, only perhaps in smaller type than the antics of the great and powerful. Moreover, thousands of soldier letters, military reports, general orders, and even occasionally diaries, found their way into ink on newsprint, many of them items available nowhere else. Thanks to the policy of editors exchanging newspapers among themselves and borrowing stories from each other, often newspapers for which not a single issue survives, still live in excerpts published in other journals. Even the advertisements are mirrors of consumers and their concerns in the 1860s.
The goal of the American Civil War Newspapers database is to select a representative group of journals to index, with digital images of the newspapers themselves, for use by students and scholars. The newspapers selected will be a representative sampling of Union and Confederate, urban and small town, Eastern and Western, pro– and anti–administration