What do you mean by "easier"? If programming in individual pixel access, it's simplest to treat the image as a 2D array of pixels.

If using a library like ImageMagick, they are all equally easy because you use the same API.

"better with PNG" isn't just Perl, it's because libpng is promoted to go along with the png format, so any program can easily incorperate png support.

Choose PNG over GIF: well, there is a little problem with licencing fees. So you will find no (legal) free GIF software anymore, since nobody will pay $5000 to be allowed to code something which he'll then give away. PNG is better in every respect (by design) except as an animation format, so just use PNG and forget GIF.

If you just want to change a color globally, look into color-indexed modes rather than true color modes. Then you just change the value once, as the image data actually refer to the palette index.

Note that PNG allows for transparancy and alpha-blending, so maybe what you are really looking for are transparant sections?

—John