Gojuuon translates literally as 50 sounds and refers to the sounds in the Japanese language. There are more than 50 sounds, but the name comes from a chart, gojuuonhyou (五十音表), which is ten columns wide and five rows high and is used to display the basic 46 currently used characters.
Gojuuonjun (五十音順) means 50 sound order and refers to listing words in the same order as the chart. This is essentially the Japanese equivalent of alphabetizing.
Some reference books designed for use in the West have indices or glossaries arranged alphabetically, which introduces more opportunity for error because of differing systems of romanization and other issues. Learning the basic kana characters of Japanese is recommended for any serious study.