This will run nl2br on everything inside a string except for what is between the opening and closing tags. For example you can add
's to a comment that contains [ code ] tags without touching the code itself:

$comment = nl2br_excluding($comment, '\', '\[\/code\]');

The opening and closing inputs need to be backslashed and ready for a regular expression to accept them.

The reason I needed to write this was because PHP does not support variable length lookbehind assertions. So this is a solution for anybody who has come across the following error:

Compilation failed: lookbehind assertion is not fixed length

/********************************************************************************/
// Replaces newlines on everything except what is in the given tags

function nl2br_excluding($string, $open, $close) {

    $substring = array();

    // Strip the backslashes so we have a clean representation of the tags.
    $open_tag = stripslashes($open);
    $close_tag = stripslashes($close);

    $count = preg_match_all("#$open(.*?)$close#si", $string, $matches);
    for($i = 0; $i < $count; $i++) {

        // Save the substring between the tags in a numbered array.
        $substring[$i] = $matches[1][$i];

        // Replace the substring within the tags with a number so we can replace it later.
        $match = $open_tag.$substring[$i].$close_tag;
        $replace = $open_tag.$i.$close_tag;

        $string = str_replace($match, $replace, $string);
    }

    $string = nl2br($string);

    // After replacing the newlines go back through our substring array and put them back
    // based on their key values.

    foreach($substring as $i => $value) {
        $match = $open_tag.$i.$close_tag;
        $replace = $open_tag.$value.$close_tag;
        $string = str_replace($match, $replace, $string);
    }

    return $string;
}