I find the default cygwin color palette to be a bit ugly, so here’s one that has softer colors. Add the following lines to your .minttyrc and restart cygwin in order to apply changes.

ForegroundColour = 131, 148, 150
BackgroundColour =   0,   0,   0
CursorColour     = 220,  50,  47

Black            =   7,  54,  66
BoldBlack        =   0,  43,  54
Red              = 220,  50,  47
BoldRed          = 203,  75,  22
Green            =   0, 200, 132
BoldGreen        =   0, 200, 132
Yellow           = 204, 204, 102
BoldYellow       = 204, 204, 102
Blue             = 102, 153, 204
BoldBlue         = 102, 153, 204
Magenta          = 211,  54, 130
BoldMagenta      = 108, 113, 196
Cyan             =  42, 161, 152
BoldCyan         = 147, 161, 161
White            = 238, 232, 213
BoldWhite        = 253, 246, 227

Update (December 2018): This theme is now packaged with the default Mintty distribution! Pull up Mintty/Cygwin and check for a theme called rosipov (I didn’t pick the name).

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