Seconding Cafe Sunflower. Also, I know a lot of people like Soul Vegetarian on North Highland, or R. Thomas.
But honestly, most restaurants in the city have really good vegetarian options on the menu - the vegetable plate at upscale restaurants has evolved. Even the bars I go to almost always have a decent veggie burger and a couple other vegetarian plates.
Soul Vegetarian No Two
652 N Highland Ave NE, Atlanta, GA 30306
R Thomas Deluxe Grill
1812 Peachtree St NW, Atlanta, GA 30309
2140 Peachtree Rd NW Ste 105, Atlanta, GA 30309