I have a Kinesis Classic Contoured PS/2 Keyboard (KB133PC) which I use via a PS/2 -> USB converter with my Mac Book Pro. I just upgraded to Snow Leopard, and it completely forgot my custom mapping: right Alt key to Right Command. Documenting the process here to not have to re discover it.

The process:

1. System Preferences > Keyboard > Modifier Keys

2. Choose Non-Apple Internal Keyboard

3. Switch one of the settings here to see what it drops in ~/Library/Preferences/ByHost/.GlobalPreferences*

4.Convert the file using:

 plutil -convert xml1 -o  .GlobalPreferences.*

5. Hack the XML to look something like:

    <key>com.apple.keyboard.modifiermapping.1241-5120-0</key>
    <array>
        <dict>
            <key>HIDKeyboardModifierMappingDst</key>
            <integer>12</integer>
            <key>HIDKeyboardModifierMappingSrc</key>
            <integer>11</integer>
        </dict>
    </array>

6. Convert it back:

 plutil -convert binary1 -o .bin 

7. Copy the .bin file over the .GlobalPreferences* file

8. Log out and back in

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