For the two compare tools in Database Workbench (File Compare and Schema Compare), you can edit the line background colors for added, modified or deleted lines here.
Either select one of the colors in the drop down box or use the Custom option at the bottom of the drop down list, this will show a color-picker dialog.
Color-picker dialog (number of colors reduced in this screenshot)
You can pick a color from the grid on the left or create a new color using the two colored pickers at the right. Use the Add to Custom Colors button to add the new color to the array of available custom colors.