I accidentally found out a way to organize iTunes AppleScripts. Simply adding a dash (or a minus sign) at the beginning of the script's name will place the script above other scripts -- even though the dashes won't show in iTunes AppleScripts menu. You can add more than one dash and you can create seperator by creating an empty script and naming them using dash(es). For example, here's my iTunes script folder, and the resulting menu display in iTunes.
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