Commonly, white is made transparent:
giftrans -help
Usage: giftrans [ -t #rrggbb ] [ -o newfile.gif ] [-l] oldfile.gif
Convert any GIF file into a GIF89a, making the specified:
color `transparent'. The color is specified with the -t option
followed by #rrggbb, where `rrggbb' are six hex digits which
indicate the Red-Green-Blue components.
The default color is white = #ffffff, i.e. if the
-t option is not specified, `-t #ffffff' is assumed.
Output goes to stdout unless an -o output file is
specified. The -l option lists the GIF file's color table.
OPTIONS:
-t Specify the transparent color
-o Redirect stdout to a file
-l Only list the color table