Speaking purely of atmosphere, with no consideration of food quality. Not necessarily in order.
Garden Grill: Revolving restaurant (unique at WDW), scenery from the Living with the Land attraction (rare to have a view of an attraction), and if you are seated on the lower level, you have a private booth (where else at WDW?). Add in the characters and it's atmosphere in spades.
Coral Reef: Have not eaten there but definitely a unique atmosphere.
Sci-Fi Dine-in: Obviously unique, and a lot of fun for most people.
California Grill: View from the 14th(15th?) floor, stunning both in daylight and after dark, and sunset is especially nice. Who needs fireworks?! (And the food is VERY good as well, but even with bad food it would make the atmosphere list.)
House of Blues: Best music in any WDW restaurant, and very interesting artwork on the walls.
Honorable Mention: 50s Prime Time (for those over 50, the accuracy is uncanny!), Rainforest Cafe