How do you debug PHP scripts?

You can use Firephp an add-on to firebug to debug php in the same environment as javascript.

I also use Xdebug mentioned earlier for profiling php.

This is my little debug environment:

error_reporting(-1);
assert_options(ASSERT_ACTIVE, 1);
assert_options(ASSERT_WARNING, 0);
assert_options(ASSERT_BAIL, 0);
assert_options(ASSERT_QUIET_EVAL, 0);
assert_options(ASSERT_CALLBACK, 'assert_callcack');
set_error_handler('error_handler');
set_exception_handler('exception_handler');
register_shutdown_function('shutdown_handler');

function assert_callcack($file, $line, $message) {
    throw new Customizable_Exception($message, null, $file, $line);
}

function error_handler($errno, $error, $file, $line, $vars) {
    if ($errno === 0 || ($errno & error_reporting()) === 0) {
        return;
    }

    throw new Customizable_Exception($error, $errno, $file, $line);
}

function exception_handler(Exception $e) {
    // Do what ever!
    echo '<pre>', print_r($e, true), '</pre>';
    exit;
}

function shutdown_handler() {
    try {
        if (null !== $error = error_get_last()) {
            throw new Customizable_Exception($error['message'], $error['type'], $error['file'], $error['line']);
        }
    } catch (Exception $e) {
        exception_handler($e);
    }
}

class Customizable_Exception extends Exception {
    public function __construct($message = null, $code = null, $file = null, $line = null) {
        if ($code === null) {
            parent::__construct($message);
        } else {
            parent::__construct($message, $code);
        }
        if ($file !== null) {
            $this->file = $file;
        }
        if ($line !== null) {
            $this->line = $line;
        }
    }
}

Try Eclipse PDT to setup an Eclipse environment that has debugging features like you mentioned. The ability to step into the code is a much better way to debug then the old method of var_dump and print at various points to see where your flow goes wrong. When all else fails though and all I have is SSH and vim I still var_dump()/die() to find where the code goes south.