These games went through significant changes when undergoing the localization process from one region to another. This can range from just changing a weird region-specific joke to something more accessible, to outright censorship of more mature content.
In some cases, games even go through major improvements whilst undergoing the localization process, as the developers use the extra time to fix and enhance things they didn't quite get right the first time around. Sometimes these upgraded translations get re-translated to the original country with improvements intact! (See: Final Fantasy VII International or Shindou Super Mario 64.)