Since there is no official layout for the mountain I've put together a rough idea of what would be on which levels. Keeping in mind that the most important rooms/halls would be the best guarded, and therefore, furthest inward. I tried to match what was shown in the movies, but there wasn't a lot to go by.
By the Entrance: Gate, Stables
Closest to the Rock Face: Guest Quarters (have windows)
Runs Throughout: Aqueduct/Reservoir, Guard Stations, Mail Service(?), Park Equivalent(?), Sanitation
Each can span multiple levels:
(Top)
Farms
3-4 levels: Bathing Hall, Great Hall (dining), Residential
3-4 levels: Arena/Theater, Bank, Guild Hall, Market
(Entrance level): Food Processing, Food Storage, Hall of Healing(hospital), Hall of Learning (school), Throne
Armory, Brewery, Laundry, Training Arena
Government Center, Hall of Knowledge (library), Treasury
Forges, Hall of Kings, Mine Entrance
(Bottom)
I think that's everything. I'm unsure about the idea of farms in a mountain but I can't imagine the Dwarves relying on other races for necessities or having farms outside of the mountain where they would be vulnerable. It seems that it is commonly accepted that Dwarves in mountains would grow the equivalent of cave plants; fungus, moss, etc.
I'm thinking on a grander scale. In the movies, we see Dwarf women selling clothe in the market of Dale. In order to have textiles to sell, they would have to grow their own materials. That means farms with sheep, or cotton, or silk, or so on. The farms would have to be close to the surface to more easily get light and I'm thinking that the Dwarves would be clever enough to find a way, through mirrors or crystals or some combination of the two, to get enough sunlight into the mountain to grow things. That, or they have a light source that would work as a substitute. Every shot we saw of the inside of Erebor was impressively lit.
So, that's my layout and I'm sticking to it. I probably won't get too into the intricacies of the layout in my stories, but at least it's there for consistencies sake.
Update: Made a rough visual