3. Fitzgerald's: God knows the sound wasn't always great at Fitz, upstairs or down. Downstairs, there are still issues, but the improvement in the upstairs room since it was bought has been marked. The building's all-wood interior is well-suited for live sound and even when it is loud in there, it isn't painful.
I remember when the sound in there was questionable at best. Now, it's downright great. Whether it's some loud metal band or a twee hipster acoustic duo, Fitz makes it sound great no matter where you sit or stand in the room, including the balcony, and that is not an easy thing to do.
2. Continental Club: I honestly don't think Continental gets nearly enough praise for how good it sounds inside. It might be the warmest sound system in the city, especially given the high ceilings and concrete floors.
I've rarely been there when vocals weren't clear and when the sound was loud enough to stifle virtually everything else, but clear enough that it didn't make ears bleed. Hell, it even sounds good sitting on the porch at Double Trouble next door.