I believe there is a civil rights museum located near MLKs gravesite, but I'm not 100% certain. Atlantans, help us out here!
The High Museum is the major art museum...and it sucks. There is a new museum called The Contemporary and I have heard that it is not so great - it is only a local artist venue. The Carlos Museum on Emory's campus has a great collection of Egyptian art and the building is a trip because it was designed by postmodern architect Michael Graves...so if you want to see really ugly wall colors, go there. Fernbank Museum is a really good natural history museum. The Center for Puppetry Arts has a small museum with some cool puppets, but I don't think it would be worth it just for the museum - you would have to see a show there, as well - they have adult and children's shows. There is something called Sciteck, or something...on Piedmont south of Ponce - some kind of science and technology museum that is supposed to be very good. The museum at Clark Atlanta University has a great African-American art collection. For the most part, cultural attractions in Atlanta suck, but the science/history museums are pretty good, especially if it is Southern specific.