Usually when I research, I have a bunch of windows open. Aside from my tree at ancestry and it's search functions, I normally am also using familysearch.org. Whether its using their search functions, or browsing their records for probate (recently added to Ancestry also) information. Then of course there is fold3 which I use for Dawes files and for military records. I know many are on Ancestry, but I like the browse feature to narrow my search better there.
Okay, then there of course is google. I google a lot. I especially like using the book tab under googles. Sometimes it is only an excerpt, but you can find some real gems on google. Old books on genealogy, well don't forget to visit www.archive.org. There is some great stuff on there as well.
For newspapers, well, I have to admit, I have subscriptions to genealogybank, newspapers.com, and newspaperarchives.com. But there are some great free sites too. Some papers are available for each state at the Chronicling America, but there are a few lesser known sites.
Upper New York newspapers are here and this great site by a private individual Fulton Postcards.
State Archives with digital content (awesome content) that I visit often.
Georgia Archives (newspapers require Firefox, won't work now with google or windows Edge)
South Carolina Archives
Florida Memory Projects
Virginia Chancery Cases
For early tax lists of Virginia, this is a great site.
US genweb I use too, but some sites are better than others. Don't miss the Santa Rosa or Escambia sites, they both have some great information.
Accessgenealogy has some great stuff too. Don't miss the McMinn County, Tennessee transcriptions there.
Most people don't realize the 1885 annuity roll (mislabeled as a census) is on fold3 and on Ancestry under the U.S. Indian Rolls. The counties aren't labeled, but the file you want is the Union file, that is the 1885 Choctaw census. Some of the early censuses for the counties are on Ancestry, as well as probate records and court records for a few of the counties, but they aren't searchable. You have to browse each roll. The Collection for those records is found here. You have to use the browse function to find the Choctaw rolls. Roll 1 is Mississippi Choctaw related. Roll 4 is Choctaw citizenship related. Rolls 2 and 3 have census data. The Carton's (ctn) files are the court records.
Most people also don't realize there are some Alabama Territorial records in the Mississippi records on familysearch. You have to look at the counties and browse, but early tax lists can be found there. The collection you want is here.