As of Version 6.0, HiddenSurface -> False has been superseded by the setting PlotStyle -> FaceForm[].
HTMLSave is superseded by Export[..., "HTML"] in Version 6.
As of Version 6.0, ImageRotated has been superseded by the "ImageTopOrientation" element specification.
As of Version 6.0, LightSources has been superseded by settings for Lighting.
As of Version 6.0, PolygonIntersections has been superseded by various options for Export.
As of Version 6.0, RenderAll has been rendered obsolete by the symbolic representation of graphics in Mathematica.
Since Version 5.0 (released in 2003), SingularValues has been superseded by SingularValueList and SingularValueDecomposition.
As of Version 6.0, SurfaceGraphics has been superseded by GraphicsComplex and related functionality.
As of Version 6.0, TextStyle has been superseded by BaseStyle, LabelStyle and other options.
As of Mathematica 7, ToFileName has been superseded by FileNameJoin.