The solution

  1. The Mathematica fonts need to be present on the X server. Copy them from the X client (that has the Mathematica binaries) to the X server:

    scp -r /opt/Mathematica-6.0/SystemFiles/Fonts/Type1 user@othermachine:~/MathFonts

  2. On the X server, add the new font directory to your font path:

    xset fp+ ~/MathFonts

  3. Start Mathematica. Half of the error message will still show up, but the program will start and run.

[Note]Note

As a side note: as of version 6.0, the IWI license server has been replaced with the University wide one.