JSL is the romanization system used in the textbook series Japanese: the spoken language by Eleanor Harz Jorden. It is based on the format of Kunrei romanization, with the difference that long vowels are written using doubled vowels, such as "oo" or "uu", rather than macrons or circumflexes, and the addition of information on pitch accent using acute, grave and circumflex marks. JSL romanization is intended for language teaching and study.
99 shiki is a form of romanization developed from the view of romaji as a means of transliteration rather than as a strict orthography. As such it allows romanization of variant kana forms which do not currently have a romanized form. It uses neither circumflexes nor macrons.
In practice the most widely used romanization in Japan is an unnamed variant of Hepburn romanization sometimes described as "easy-to-read" romanization. In this form of romanization, long vowels and syllabic ns are simply not indicated at all. This type of romanization is used in train stations to indicate station names, and it is the form of romanization which gives us Tokyo and Kyoto for the Japanese cities.