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gnuplot supports transparency in some cases, but not for simple lines. It would be helpful to be able to do something like 'plot x lc rgba "#AABBCC00"' to plot transparent lines on top of each other.
This feature is already present in the current development version (4.7).
gnuplot> help rgbcolor
"#AARRGGBB" represents an RGB color with an alpha channel (transparency)
value in the high bits. An alpha value of 0 represents a fully opaque color;
i.e., "#00RRGGBB" is the same as "#RRGGBB". An alpha value of 255 (FF)
represents full transparency. `Note`: This convention for the alpha channel
is backwards from that used by the "with rgbalpha" image plot mode in earlier
versions of gnuplot.
There is now a demo for transparent lines in the on-line collection