It was in Yesterday's Enteprrise. So were the bridges of the Enterprise-C, the Hathaway and the Stargazer. USS Voyager is the most dramatic by far; the upper level is a good three feet higher than the lower level and Tom's helm station is basically a hole in the ground. And though it's not a starship, the DS9 Ops deck actually made this concept explicit, placing the commander's office high above the rest of the floor "so subordinates have to look up with respect."
I'd also say the bridge of the original Enterprise had two levels.
