Most researchers know that if they have a Union Civil War ancestor, chances are he, his widow, his elderly parents, or the guardian of his orphaned child(ren) applied for a pension in his name; and that copies of these pension applications are available for a fee of $75 from the National Archives. Unlike military service records, pension records are chock-full of genealogical information, as the applicants had to prove there was no one in the family that could support them, or--in the case of widows, parents and orphans--that they were related to the deceased veteran.
What researchers often don't realize is that many Confederate veterans were also eligible for pensions; no, not from the Federal Government--the government against which they had waged war--but from a former Confederate state. The veteran had to apply to the state in which he currently resided after the war...not necessarily the state from which he served. Obviously, then, if the veteran resided in a Union state after the war, or a location that saw statehood after 1865, he would not have been eligible for a pension. Our family's only Confederate ancestor, my husband's 2nd-great-grandfather, Charles Anderson Midkiff, served in the Texas Cavalry and would not have received a pension. He lived in Colorado and California in his later years: a Union state and former territory, respectively.
One of my students requested some extra help in researching her Civil War ancestors. I helped her order her Union ancestor's pension record online at the NARA site, and then we searched the Texas Confederate Pension database online for her Confederate ancestor (no luck). I realized that there should be a list online somewhere that would have all the links for any online Confederate Pension databases, and I was right. Joe Beine had a list of where to order pension records (Union and Confederate) among all his great online military records links. I also found a list of where to order Confederate pension records with descriptive information on Troy Grove's Terry's Texas Rangers website. The descriptions include when pensions begin and who was eligible (the veteran only, widows, etc.). Each list has a few things the other didn't, and as often happens, some of the links were obsolete (neither Joe's nor Troy's fault; government websites are notorious for changing their pages' URLs, I've noticed). NARA also has a descriptive list and includes mail, phone and e-mail information for each archive office for the states that granted Confederate pensions. Again, some of their links are obsolete.
I decided to put together my own list of online Confederate veterans pension application databases, many from the former Confederate states' archives, shown below. Once you find your ancestor in the database, there is information on each website to help you order a copy of his pension application and record.
Alabama - The archives do not have an online pension application database. They do have a database of those who served from Alabama here, as well as those individuals who were exempted from service or who served in the militia or home guard. Contact information for the archives can be found on the bottom of the home page here.
Arkansas - State archives: http://www.ark-ives.com/documenting/confed_pensions.asp. FamilySearch has Arkansas Confederate Pensions, 1901-1929.
Florida - State archives: http://www.floridamemory.com/Collections/PensionFiles/. Family Search has Florida, Confederate Veterans and Widows Pension Applications, 1885-1955.
Georgia - http://cdm.sos.state.ga.us/cdm4/TestApps.php. Ancestry now has the Georgia, Confederate Pensions Applications, 1879 - 1960 database available in their subscription area.
Louisiana - State archives: http://www400.sos.louisiana.gov/archives/gen/cpa-alpha.htm - this is a fairly new link to the pension applications index. A form to request a copy of the pension application can be downloaded here. FamilySearch has Louisiana Confederate Pensions,1898-1950.
Mississippi - Research requests information can be found here at the Mississippi State Archives (does not have records or indexes online). FamilySearch has Mississippi Confederate Veterans and Widows Pension Applications, 1900-1974.
North Carolina - http://mars.archives.ncdcr.gov/BasicSearch.aspx - because this search engine is rather complicated, I recommend viewing the Manuscript and Archives Reference System (MARS) video tutorials found on YouTube here. Also, FamilySearch has North Carolina, Confederate Soldiers and Widows Pension Applications, 1885-1953.
South Carolina - http://www.archivesindex.sc.gov/onlinearchives/search.aspx - choose Records of Confederate Veterans, 1909 - 1973 from the drop down menu under the Record Group field.
Another search: http://22.214.171.124/search2.aspx - click on Search for names in the upper left-hand corner to find your Confederate ancestor.
Try both search engines; in the past, I got different results using the same search terms on each search engine. Online request forms can be accessed here. Be sure to list that your request is for a pension application record, or you may be sent a military service record instead.
Tennessee - http://www.tennessee.gov/tsla/history/military/pension.htm. Also FamilySearch has Tennessee, Confederate Pension Applications, Soldiers and Widows, 1891-1965.
Texas - https://www.tsl.state.tx.us/apps/arc/pensions/. Also, Ancestry has a database titled U.S., Confederate Pensions, 1884-1958 that appears to contain names from "Texas, Confederate Pension Applications, 1899-1975. Vol. 1–646 & 1–283" from the Texas State Library and Archives Commission in Austin.
Virginia - http://www.lva.lib.va.us/whatwehave/mil/ - this page includes a link not just to the pension rolls, but to the electronic card index, the disability applications and receipts, and applications for admission to the Robert E. Lee Camp Confederate Soldiers' Home, as well as other Civil War military links. There are military links for many other wars, too. Also, Ancestry has a database titled U.S., Confederate Pensions, 1884-1958 that appears to contain names from "Confederate Pension Rolls, Veterans and Widows" from the Library of Virginia in Richmond.
Kentucky, Missouri, and Oklahoma granted pensions to its Confederate veterans after the war. Oklahoma was known as Indian Territory during the war, and its tribal governments supported the Confederacy. Kentucky and Missouri both had populations with strong Southern sympathies, rump (rival) governments, were admitted to the Confederacy, and had volunteer units which served in the Confederate Army. However, they were never under complete Confederate control and their Confederate governments ended up in exile.
Kentucky - FamilySearch has Kentucky, Confederate Pension Applications, 1912-1950.
Missouri - FamilySearch has Missouri, Confederate Pension Applications and Soldiers Home Applications.
Oklahoma - http://www.odl.state.ok.us/oar/docs/pension.pdf - this index is in .pdf format, and you will need to use the Find feature or scroll through 164 pages to find your ancestor! Contact information for ordering copies of the pension applications can be found in the left-hand menu here.
In the event that you're reading this post long after I've written it, and you discover an obsolete link, do as I did: go to Google and enter the search term:
"nameofstate state archives"
Please use the actual name of the state (Georgia, Texas, etc.) in place of nameofstate! Then use the archives website's site map or search engine to find confederate pensions. If that's no help, return to Google and enter the following term:
"confederate pension" site:http://statearchiveURL.gov
Of course, you'll enter the actual address of the state archive's website in place of http://statearchiveURL.gov! Just make sure to have the word site and the colon (:) directly in front of the address, with no spaces in between. This should help you find an updated link to the pension database just in case, as I said, the link becomes obsolete in the future.