In the lobby of the building are sixteen mailboxes, indicating that there are sixteen apartments. Leonard and Sheldon's is the top left. Penny's moves around a little. In 0109, it's on the far right of the top row. In the second season, it's next to Leonard and Sheldon's, second from the left on the top row (0209, 0214).
The mailboxes on the set are numbered 1A through 1D on the bottom row, 2A through 2D on the second row, 3A through 3D on the the third row, and 4A through 4D on the top row. This doesn't work with what we know of the layout of the building.
See also stealing snail mail.