Best way to allow plugins for a PHP application

You could use an Observer pattern. A simple functional way to accomplish this:

<?php

/** Plugin system **/

$listeners = array();

/* Create an entry point for plugins */
function hook() {
    global $listeners;

    $num_args = func_num_args();
    $args = func_get_args();

    if($num_args < 2)
        trigger_error("Insufficient arguments", E_USER_ERROR);

    // Hook name should always be first argument
    $hook_name = array_shift($args);

    if(!isset($listeners[$hook_name]))
        return; // No plugins have registered this hook

    foreach($listeners[$hook_name] as $func) {
        $args = $func($args); 
    }
    return $args;
}

/* Attach a function to a hook */
function add_listener($hook, $function_name) {
    global $listeners;
    $listeners[$hook][] = $function_name;
}

/////////////////////////

/** Sample Plugin **/
add_listener('a_b', 'my_plugin_func1');
add_listener('str', 'my_plugin_func2');

function my_plugin_func1($args) {
    return array(4, 5);
}

function my_plugin_func2($args) {
    return str_replace('sample', 'CRAZY', $args[0]);
}

/////////////////////////

/** Sample Application **/

$a = 1;
$b = 2;

list($a, $b) = hook('a_b', $a, $b);

$str  = "This is my sample application\n";
$str .= "$a + $b = ".($a+$b)."\n";
$str .= "$a * $b = ".($a*$b)."\n";

$str = hook('str', $str);
echo $str;
?>

Output:

This is my CRAZY application
4 + 5 = 9
4 * 5 = 20

Notes:

For this example source code, you must declare all your plugins before the actual source code that you want to be extendable. I’ve included an example of how to handle single or multiple values being passed to the plugin. The hardest part of this is writing the actual documentation which lists what arguments get passed to each hook.

This is just one method of accomplishing a plugin system in PHP. There are better alternatives, I suggest you check out the WordPress Documentation for more information.