Local Three is pretty good...I've only been there once though. It has a nice selection, however no where in ATL will have as good a selection as many of us have at home!
H. Harper Station has a good selection according to their online menu, but I've never been there. I don't know how up-to-date the drink menu is either.
http://hharperstation.com/downloads/drinkmenu.pdf
If you ever get up north of the city to Roswell there are a couple of places with a very good bourbon selection in downtown Roswell (on Canton Street). I don't know if you ever get up that way but there are some very good restaurants on that street. By far the best bourbon selection is Little Alley Steak and their whiskey menu even separates wheated bourbon from ryed small batch bourbon from single barrels from cask strength (although they incorrectly label the PHC as a wheated bourbon). They have PVW23 (and PVW20, I think), ORVW, PHC Cognac finish, Ritt BIB, FRSmB, and a number of other bottles. I usually opt for the ETL or FRSmB because it's not as overpriced as some of the others. It's a nice bar, with actual whiskey glasses to drink out of, instead of the standard double old fashioned glass (they use the Riedel Single Malt glass for their whiskey). It's worth checking out if you're up in that area.
http://littlealleysteak.com/menu/whiskey-menu/
The other restaurant in that area with a bourbon bar is Table and Main. They carry the FRSB, FRSmB, a couple of High West selections, a couple BMH selections, etc. Not as many options as Little Alley Steak, but more than the standard JD/MM/KC options.
http://tableandmain.com/bourbon-bar.php
*This probably goes without saying, but obviously both bourbon menus can change according to availability, so if you're looking to try a specific bourbon on this list I'd call first.