Several international organizations (the EU, UN, and Interpol) issue travel documents which can be recognized like passports even though they don't have military control over any territory.
People from American Samoa are US nationals but not US Citizens, and get a different US Passport[1]. Apparently the ILO issues travel documents, too although it is unclear how widely they are recognized[2]
[1] https://en.wikipedia.org/wiki/Travel_document#American_Samoa
[2] https://en.wikipedia.org/wiki/Travel_document#UN_travel_docu..., http://www.icao.int/Meetings/TAG-MRTD/Documents/Tag-Mrtd-20/...