Well, by default "All My Files" seems to display only files whose kind/type is known to Apple (e.g. *.pdf, *.txt, etc). It is, however, possible to customize what kind of files are displayed via "Show Search Criteria". E.g. removing all the default criteria and adding "Name" "ends with" ".graphml" as the only search criterion will display all the *.graphml files (and only those) on your machine.
That said, if you select "Documents" form the side bar and navigate to a folder that contains *.graphml files, those *.graphml files will/should be displayed by default.