I recently found out that Jordan (the country) is spelt ヨルダン, not ジョーダン, which is how it's spelt in a person's name.
Is this based on how it's pronounced in Arabic and/or Hebrew, or how it's pronounced in a European language other than English?
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Wikipedia says that Jordan was indeed ジョルダン(・ハシェミット王国) until 2003, when the Ministry of Foreign Affairs changed it to ヨルダン(・ハシェミット王国).
Jordan is not pronounced ヨルダン in either Hebrew or Arabic (see Wikipedia for a romanization), but in Hebrew the J is [j] rather than a [dʒ]. Whether the change ジョ > ヨ occurred because J was known as [j] from Hebrew (via the Latin Bible: Iordanis "River Jordan" > ヨルダン川, see Chocolate's comment below; also cf. ユダヤ人 "Jew"), from loanwords from Germanic languages (like Dutch, German, Scandinavian languages) or from all of those together is unclear. What seems to be clear, however, is that the Japanese regarded ヨ to be the more natural choice for the transcription of Jordan into カタカナ, when the Ministry of Foreign Affairs decided to change ジョルダン to ヨルダン, together with 59 other country names and 88 place names. (See this archived newspost from the 朝日新聞). The people of Japan had apparently been complaining that the Ministry of Foreign Affairs was spelling country and place names differently from everybody else.