1. A method for associating metadata to a document via flags, the method comprising: receiving a first document via a first software application user interface; providing at least one flag type for application to the first document, wherein the at least one flag type is independent of any file type; receiving a selection of a first flag for application to the first document, wherein the first flag is independent of a file type of the first document; saving metadata associated with the first flag to the first document, wherein the metadata points to the first flag that is independent of the file type of the first document in order to establish a peer reference relationship between the first document and the first flag; receiving a selection of an object that forms a portion of the first document; receiving a selection of a second flag for application to the object in the first document, wherein the second flag is independent of a file type of the embedded object; applying the second flag to the object; in response to applying the second flag to the object, indicating, with an icon in the document, that the object is an embedded flagged document object; saving metadata associated with the second flag to the embedded flagged document object of the first document, wherein the metadata points to the second flag that is independent of the file type of the embedded flagged document object in order to establish a peer reference relationship between the embedded flagged document object and the second flag; accessing a second document via a second software application user interface, wherein the second software application user interface is different than the first software application user interface; receiving a selection of a flag type via the second software application user interface; when the metadata associated with the first flag of the first document is of the selected flag type, displaying, on the second software application user interface, the metadata associated with the first flag of the first document; and when the metadata associated with the second flag of the first document is of the selected flag type, displaying, on the second software application user interface, the metadata associated with the second flag of the first document.