At the SC Genelaogical conference there was an excellent session on Cherokee ancestor research. Paul Graham presented and he really provided alot of useful and sensible information that I am sharing with all of you.
In 1934 the federal government gave tribes the right to determine their own membership. This web site at the Department of the Interior provides contact information for recognized tribes. Researchers should contact the tribe for requirements: http://www.doi.gov/cheeroke.html
If the Cherokee ancestor chose to assimilate into white culture it will be extremely difficult to document that person. However, if you would like to check and see if an Indian ancestor had any relationship with the federal government there are a few sources to check.
During the period of Indian Removal beginning in 1831 extensive records were generated. These records relate to treaties, trade, land claims, removal to Oklahoma, allotments, military affairs, military service and pensions, trust funds, and other activities. Eastern Cherokee researchers should check the indexes for the Baker Rolls for these records. Western Cherokee should check the Dawes Rolls. The Miller Rolls and Henderson Rolls are also useful.
The indexes to these rolls are available at www.accessgenealogy.com. Footnote.com has digitized the Dawes Enrollment Cards and they also have records for the Cherokee Indian Agency 1801-1835. The full text of these rolls are also available through the National Archive: www.nara.gov.