Find a Custom Variable String within another String

A regex with capture groups should work for you (/%APP:(.*?)\|ID:([0-9]+)%/):

$string = "This is my string but it also has %APP:name_of_the_app|ID:123123123% a bunch of other stuff in it";

$apps = array();
if (preg_match_all("/%APP:(.*?)\|ID:([0-9]+)%/", $string, $matches)) {
    for ($i = 0; $i < count($matches[0]); $i++) {
        $apps[] = array(
            "name" => $matches[1][$i],
            "id"   => $matches[2][$i]
        );
    }
}
print_r($apps);

Which gives:

Array
(
    [0] => Array
        (
            [name] => name_of_the_app
            [id] => 123123123
        )

)

Alternately, you can use strpos and substr to do the same thing without specifying what the tokens are called (this would bug up if you used a percentage sign in the middle of the string, though):

<?php
    $string = "This is my string but it also has %APP:name_of_the_app|ID:123123123|whatevertoken:whatevervalue% a bunch of other stuff in it";

    $inTag = false;
    $lastOffset = 0;

    $tags = array();
    while ($position = strpos($string, "%", $offset)) {
        $offset = $position + 1;
        if ($inTag) {
            $tag = substr($string, $lastOffset, $position - $lastOffset);
            $tagsSingle = array();
            $tagExplode = explode("|", $tag);
            foreach ($tagExplode as $tagVariable) {
                $colonPosition = strpos($tagVariable, ":");
                $tagsSingle[substr($tagVariable, 0, $colonPosition)] = substr($tagVariable, $colonPosition + 1);
            }
            $tags[] = $tagsSingle;
        }
        $inTag = !$inTag;
        $lastOffset = $offset;
    }

    print_r($tags);
?>

Which gives:

Array
(
    [0] => Array
        (
            [APP] => name_of_the_app
            [ID] => 123123123
            [whatevertoken] => whatevervalue
        )

)

DEMO