My picks...
Corals: Cappucino Bay - THE Place in Atlanta for Coral, especially SPS. Prices are reasonable considering the quality and selection.
Fish: Marine Fish and Reef and Imagine Ocean - Good fish selection and prices; very knowledgeable staff. They both also have a good selection of softies and LPS corals.
Parts and Supplies: Aviarium & Fish Store and More (Tie) - either one will just about any part you might need if you have to fix something quickly.
Wasabi is right; most all of the sponsor stores are good and worth the visit. Sorry if I missed anyone

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- Michael