As of Version 6.0, PlotDivision has been superseded by MaxRecursion.
As of Version 3, $DefaultFont has been superseded by settings in notebook stylesheets, and as of Version 6 by options such as BaseStyle.
Since Version 5.0 (released in 2003), $TopDirectory has been superseded by $InstallationDirectory and $BaseDirectory.
As of Version 6.0, LongestMatch has been superseded by the pattern object Longest.
As of Version 6.0, ShortestMatch has been superseded by the pattern object Shortest.
Since Version 5.0 (released in 2003), TensorRank has been superseded by ArrayDepth.
In Version 6.0, RandomPermutation1 has been superseded by RandomPermutation.
In Version 6.0, RandomPermutation2 has been superseded by RandomPermutation.
In Mathematica 6.0, ButtonMargins has been superseded by the FrameMargins option of Button.
As of Version 6.0, HiddenSurface -> False has been superseded by the setting PlotStyle -> FaceForm[].