If the image is in one of the forms supported by GD, then once you have loaded the image in the usual way, then you can use getPixel( x, y ) to obtain the color value. From the docs:

$index = $image->getPixel(x,y) object method 

This returns the color table index underneath the specified point. 
It can be combined with rgb() to obtain the rgb color underneath the p
+ixel.

Example:

        $index = $myImage->getPixel(20,100);
        ($r,$g,$b) = $myImage->rgb($index);
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By the way, I fixed up an additional alpha() method to complement rgb() in Geo::GD::Image

In GD - Is there a way to *retrieve* the alpha value of a pixel? I can do $i = $img->getPixel($x,$y); and use rgb() to get its rgb value, and the perldoc says something about hexadecimal strings carrying it. But I can't see a way to extract the hex-string. Everything seems to be concentrated on drawing, rather than extracting values from pictures.

pixels are opaque, they don't have alpha values, read http://search.cpan.org/perldoc/GD#Alpha_channels to learn how it works

You've been given a few excellent answers to your question already, but I'd like to suggest that if you're manipulating images, you might want to do so in a vector sort of way. Check out PDL from CPAN or the PDL home page if you haven't already.

sub get_pixel($$) 
{
      my ( $x, $y) = @_; 
      substr ( $image, $y * $height + $x, 1);
}
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I know this is over-simplification, but I use these direct memory hacks once in a while, f.ex. $image = ~$image for images of cardinal pixels is as valid and fast as any other image negation. Your pixel extraction problem might just as well hit the same area.

Otherwise, of course, a number of libraries provide generic image access, as mentioned above.