User blog comment:VegasFox/Good Spriters?/@comment-3190872-20120102224902/@comment-1942179-20120102234052

Or even better. Put the color you want to replace on the right click, and the color you want to replace it with on the left click. Use the select tool and select the whole sprite. Make sure you have the transparency option on, which makes the right clicked color transparent when using the select tool. Cut the sprite, and it'll leave a box with the color you want to replace there. Use the bucket tool and fill it in with the color you want, and then paste it over it. All of that color has been replaced in one fell swoop.

Rinse and repeat, and you have a perfectly clean recolored sprite. =P