1. A system for creating a backup copy of application-generated data objects, the system comprising: computer readable memory comprising at least a first de-duplication database, the first de-duplication database associated with first application-specific data, the first application-specific data comprising a first plurality of data objects generated by at least first and second clients; at least first and second data agents, the first data agent in communication with at least the first client, and the second data agent in communication with at least the second client, the first and second data agents comprising one or more computer processors comprising computer hardware, the first and second data agents monitor the first application-specific data created by the at least first and second clients and insert headers comprising de-duplication indicators in the first application-specific data to identify portions of the first plurality of data objects to be processed for duplicate data, the first application-specific data further comprising metadata associated with one or more of the first plurality of data objects, wherein the metadata further identifies at least the first and second clients, wherein one or more of the de-duplication indicators comprises an offset value identifying a beginning of at least the portions of the first plurality of data objects within the first application-specific data; the at least one media agent executing on one or more computer processors, the at least one media agent manages a backup of the first application-specific data, the headers comprising the de-duplication indicators, and the metadata received from the first and second data agents; a de-duplication module that communicates with the media agent, the de-duplication module executing on one or more computer processors comprising computer hardware, the de-duplication module receives the application-specific data from the media agent and performs block-level de-duplication on the first application-specific data as part of the backup of the first application-specific data, the de-duplication module further configured to: use the inserted headers comprising the de-duplication indicators to identify the beginning of at least one of a first portion of the first plurality of data objects from the first client based on the offset value; and determine if a duplicate copy of blocks associated with the first portion of the first plurality of data objects from the first client exist in the first de-duplication database; and if a duplicate copy does not exist in the first de-duplication database, storing the first portion of the blocks in the first de-duplication database and storing first metadata that identifies the first client in associated with the duplicate copy; determine if a duplicate copy of any of blocks associated with a second portion of the first plurality of data objects from the second client exist in the first de-duplication database; if a duplicate copy exists in the first de-duplication database, removing the duplicate data in the second portion the first application-specific data associated with the second client; determining whether second metadata in the second portion of the first application-specific data that identifies the second client is unique; and if the second metadata is unique, creating a backup copy of the second metadata in association with the duplicate copy in the first de-duplication database, wherein the backup copy stores multiple instances of differing metadata associated with the duplicate copy wherein the first metadata that identifies the first client and the second metadata that identifies the second client are stored in association with the duplicate copy.