As of Mathematica 7, ToFileName has been superseded by FileNameJoin.
As of Version 3, $DefaultFont has been superseded by settings in notebook stylesheets, and as of Version 6 by options such as BaseStyle.
As of version 6.0, $FormatType has been superseded by explicit settings for FormatType in Graphics and related functions.
As of Version 6.0, $MachineDomain has been superseded by $MachineDomains.
As of Version 6.0, $ProductInformation has been superseded by SystemInformation.
As of Version 6.0, $RandomState has been superseded by the scoping construct BlockRandom.
As of Mathematica 7.0, $TemporaryPrefix has been superseded by $TemporaryDirectory.
As of Version 6.0, $TextStyle has been superseded by BaseStyle and other options.