Gerber files, also known as RS-274 files, are the standard file interchange format for circuit board manufacturing.
The most modern form of Gerber files are known as RS-274X and have embedded aperture codes, meaning that the file is fully self-contained and no external aperture file is needed. ["Eagle"] generates RS-274X Gerber files using the GERBER_RS274X device in the CAM processor. Probably the best description of the RS-274X format is found in this [http://www.maniabarco.com/transdown/rs274xrevd_e.pdf this document] from Mania Barco.
All layers of the board have their own Gerber file. Non-board layers, such as fabrication drawings, etc. are also sent as Gerber files.
The one exception to this rule is the drill file. This file is usually sent in Excellon format. The Excellon drill file indicates where on the board to drill and with which drill size.