Be aware that

<?php
$rgba     = imagecolorat($image, $x, $y);
$r = ($rgba >> 16) & 0xFF;
$g = ($rgba >> 8) & 0xFF;
$b = $rgba & 0xFF;
$a     = ($rgba & 0x7F000000) >> 24;
?> 

will only work for truecolor images. With eg GIF images, this will have strange results. For GIF images, you should always use imagecolorsforindex().

If you would like to change the intensity or lightness level of a specific color, you will need to convert the color format from RGB to HSL. 
following function convert RGB array(red,green,blue) to HSL array(hue, saturation, lightness)
<?php
/**
 * Convert RGB colors array into HSL array
 * 
 * @param array $ RGB colors set
 * @return array HSL set
 */
 function rgb2hsl($rgb){
    
     $clrR = ($rgb[0] / 255);
     $clrG = ($rgb[1] / 255);
     $clrB = ($rgb[2] / 255);
    
     $clrMin = min($clrR, $clrG, $clrB);
     $clrMax = max($clrR, $clrG, $clrB);
     $deltaMax = $clrMax - $clrMin;
    
     $L = ($clrMax + $clrMin) / 2;
    
     if (0 == $deltaMax){
         $H = 0;
         $S = 0;
         }
    else{
         if (0.5 > $L){
             $S = $deltaMax / ($clrMax + $clrMin);
             }
        else{
             $S = $deltaMax / (2 - $clrMax - $clrMin);
             }
         $deltaR = ((($clrMax - $clrR) / 6) + ($deltaMax / 2)) / $deltaMax;
         $deltaG = ((($clrMax - $clrG) / 6) + ($deltaMax / 2)) / $deltaMax;
         $deltaB = ((($clrMax - $clrB) / 6) + ($deltaMax / 2)) / $deltaMax;
         if ($clrR == $clrMax){
             $H = $deltaB - $deltaG;
             }
        else if ($clrG == $clrMax){
             $H = (1 / 3) + $deltaR - $deltaB;
             }
        else if ($clrB == $clrMax){
             $H = (2 / 3) + $deltaG - $deltaR;
             }
         if (0 > $H) $H += 1;
         if (1 < $H) $H -= 1;
         }
     return array($H, $S, $L);
     }
?>

While it's quite easy and intuitive to get the alpha transparency of a pixel with:

<?php
$rgba     = imagecolorsforindex($image, imagecolorat($image, $x, $y));
$alpha     = $rgba["alpha"];
?>

you should use the return value of the command imagecolorat to get the alpha transparency with the code below because it's much faster and will have a major impact if you process every pixel of an image:

<?php
$rgba     = imagecolorat($image, $x, $y);
$alpha     = ($rgba & 0x7F000000) >> 24;
?>

I have optimized the rgb2hsl function from slepichev a bit, so that it is a bit shorter and hopefully a bit faster:

<?php
/**
 * Convert RGB colors array into HSL array
 * 
 * @param array $ RGB colors set, each color component with range 0 to 255
 * @return array HSL set, each color component with range 0 to 1
 */
function rgb2hsl($rgb){
    $clrR = ($rgb[0]);
    $clrG = ($rgb[1]);
    $clrB = ($rgb[2]);
     
    $clrMin = min($clrR, $clrG, $clrB);
    $clrMax = max($clrR, $clrG, $clrB);
    $deltaMax = $clrMax - $clrMin;
     
    $L = ($clrMax + $clrMin) / 510;
     
    if (0 == $deltaMax){
        $H = 0;
        $S = 0;
    }
    else{
        if (0.5 > $L){
            $S = $deltaMax / ($clrMax + $clrMin);
        }
        else{
            $S = $deltaMax / (510 - $clrMax - $clrMin);
        }

        if ($clrMax == $clrR) {
            $H = ($clrG - $clrB) / (6.0 * $deltaMax);
        }
        else if ($clrMax == $clrG) {
            $H = 1/3 + ($clrB - $clrR) / (6.0 * $deltaMax);
        }
        else {
            $H = 2 / 3 + ($clrR - $clrG) / (6.0 * $deltaMax);
        }

        if (0 > $H) $H += 1;
        if (1 < $H) $H -= 1;
    }
    return array($H, $S,$L);
}
?>

The earlier microsoft sepia example seemed to have a factor in which made it pinky... here is a modified example which uses just the Microsoft sepia (as per the wiki sepia entry)

<?
function imagetosepia(&$img) {
  if (!($t = imagecolorstotal($img))) {
    $t = 256;
    imagetruecolortopalette($img, true, $t);
  }
  $total = imagecolorstotal( $img );
  for ( $i = 0; $i < $total; $i++ ) {
    $index = imagecolorsforindex( $img, $i );
    $red = ( $index["red"] * 0.393 + $index["green"] * 0.769 + $index["blue"] * 0.189 );
    $green = ( $index["red"] * 0.349 + $index["green"] * 0.686 + $index["blue"] * 0.168 ); 
    $blue = ( $index["red"] * 0.272 + $index["green"] * 0.534 + $index["blue"] * 0.131 ); 
    if ($red > 255) { $red = 255; }
    if ($green > 255) { $green = 255; }
    if ($blue > 255) { $blue = 255; }
    imagecolorset( $img, $i, $red, $green, $blue );
  }
}
?>

To correct m4551 at abasoft dot it example:

ImageTrueColorToPalette($im,1,$t);

might give less colors than $t, so the for loop should call "$i<ImageColorsTotal($im)" instead of "$i<$t" just to be sure, or you'll get the warning: Color index [0-9] out of range

Regarding m4551's method of conversion -- the actual CCIR-approved RGB-to-grayscale conversion is as follows:

grayscale component = 0.2125*R + 0.7154*G + 0.0721*B

(cf. CCIR Recommendation 709 for modern monitors)

here's a function to greyscale an image even from a truecolor source (jpeg or png).

slightly poor quality, but very fast...

function imagegreyscale(&$img, $dither=1) {    
    if (!($t = imagecolorstotal($img))) {
        $t = 256;
        imagetruecolortopalette($img, $dither, $t);    
    }
    for ($c = 0; $c < $t; $c++) {    
        $col = imagecolorsforindex($img, $c);
        $min = min($col['red'],$col['green'],$col['blue']);
        $max = max($col['red'],$col['green'],$col['blue']);
        $i = ($max+$min)/2;
        imagecolorset($img, $c, $i, $i, $i);
    }
}

Here's a better grayscale, sepia, and general tinting function.  This function is better because:

1) Works with true color images (the other sepia code didn't).
2) Provides a more gooder grayscale conversion (yes, I said "more gooder").  The other grayscale code used imagetruecolortopalette, which just doesn't work well for grayscale conversion.
3) The other sepia code was really colorful, a little too much for my taste.  This function allows you to optionally set the tinting of the grayscale to anything you wish.
4) Single function for grayscale, sepia, and any other tinting you can dream up.

Here's some examples:

imagegrayscaletint ($img);  // Grayscale, no tinting
imagegrayscaletint ($img,304,242,209);  // What I use for sepia
imagegrayscaletint ($img,0,0,255);  // A berry blue image

The RGB values for tinting are normally from 0 to 255.  But, you can use values larger than 255 to lighten and "burn" the image.  The sepia example above does this a little, the below example provides a better example of lightening the image and burning the light areas out a little:

imagegrayscaletint ($img,400,400,400);  // Lighten image
imagegrayscaletint ($img,127,127,127);  // Darken image

<?
function imagegrayscaletint (&$img, $tint_r = 255, $tint_g = 255, $tint_b = 255) {
  $width = imagesx($img); $height = imagesy($img);
  $dest = imagecreate ($width, $height);
  for ($i=0; $i<256; $i++) imagecolorallocate ($dest, $i, $i, $i);
  imagecopyresized ($dest, $img, 0, 0, 0, 0, $width, $height, $width, $height);
  for ($i = 0; $i < 256; $i++) imagecolorset ($dest, $i, min($i * abs($tint_r) / 255, 255), min($i * abs($tint_g) / 255, 255), min($i * abs($tint_b) / 255, 255));
  $img = imagecreate ($width, $height);
  imagecopy ($img, $dest, 0, 0, 0, 0, $width, $height);
  imagedestroy ($dest);
}
?>

this is a sepia filter using microsoft's definition

<?php

function imagesepia( $img ) {
    $total = imagecolorstotal( $img );
    for ( $i = 0; $i < $total; $i++ ) {
        $index = imagecolorsforindex( $img, $i );
        $red = ( $index["red"] * 0.393 + $index["green"] * 0.769 + $index["blue"] * 0.189 ) / 1.351;
        $green = ( $index["red"] * 0.349 + $index["green"] * 0.686 + $index["blue"] * 0.168 ) / 1.203;
        $blue = ( $index["red"] * 0.272 + $index["green"] * 0.534 + $index["blue"] * 0.131 ) / 2.140;
        imagecolorset( $img, $i, $red, $green, $blue );
    }
}

?>