Imager is pretty good for that. For an example of manipulation see Tk ImageMap-color-zones. That just tints images. To replace some color, you could go thru every pixel, test for the rgb value to change, then adjust each pixel. I don't see anyway other than going thru the image pixel by pixel. Tinting is fast. Testing each pixel is slow.

Here is a snippet to get pixel rgb values with GD, and I'm sure Imager has a similar method.

#!/usr/bin/perl

use GD;
my $image = newFromPng GD::Image('z.png');
($x,$y)=$image->getBounds();
$maxColors = $image->colorsTotal;
$pixel=$image->getPixel(23,34);
($r,$g,$b)=$image->rgb($pixel);
print "$r\t$g\t$b\n";
[download]

And check out gif colour changes