Styx

Nice script, very useful =D

except when I run it as-is, the first line, <?php, is on the second line uncounted and line 1 is left blank

so I went ahead and made an attempt somewhat based on your script:
[php]<?php
$file = 'script.php';

ob_start();
highlight_file($file);
$source = ob_get_contents();
ob_end_clean();

echo '<pre>';
$blocks = explode("\n", $source);
$lines = str_replace('&nbsp;', ' ', explode(chr(13), $blocks[1]));
for ($i = 0; $i < count($lines); $i++)
{
for ($j = 0; $j < strlen(count($lines)) - strlen($i + 1); $j++)
{
echo '&nbsp;';
}
$lines[$i] = (($i == 0) ? '<br />' : '') . $lines[$i];
echo '<span style="color: #777777">' . ($i + 1) . '</span> ' . substr($lines[$i], 6) . "\n";
}
echo '</pre>';
?>[/php]
Notes:
replacing &nbsp; with a space reduces the file size also, there seems to be a difference between "\n" and chr(13) from highlight_file, so splitting it into blocks first with "\n" will let you get what you want (the content itself) to split it with chr(13), which removes that first extra new line.