Comment 38 for bug 197163

So, I got the font rendering right now. It seems that the version of Qt libraries supplied by Mathematica are incompatible with Hardy. This procedure worked for me:

1) Make sure you have libqt4-core and libqt4-gui installed (use synaptics or aptitude),
2) remove (delete or backup somewhere) these files:
PathToMathematica/SystemFiles/Libraries/Linux/libQtCore.so.4
PathToMathematica/SystemFiles/Libraries/Linux/libQtGui.so.4
where PathToMathematica is typicaly /usr/local/Wolfram/Mathematica/6.0
(Substitute Linux-x86-64 for Linux if needed.)

Notes:
1) I deleted ~/.fonts.conf, so fonts are set up as on a clean install of Hardy.
2) If you remove only one of these files mentioned above, then Mathematica crashes.
3) I have noticed another bug - which brought me to the idea that our problems are not only font-related - when I tried to print a notebook (File -> Print) then there were no printers in the drop down menu (any one else can confirm this?)! This issue is also solved by the procedure suggested above.

Hope it helps.