This is the best way I found to automatically run multiple commands or commands that might take longer then expected.  NOTE: this assumes that no where in the output is there the text '[end]' otherwise the function will end prematurely.  Hope this helps people.

<?php
$ip = 'ip_address';
$user = 'username';
$pass = 'password';

$connection = ssh2_connect($ip);
ssh2_auth_password($connection,$user,$pass);
$shell = ssh2_shell($connection,"bash");

//Trick is in the start and end echos which can be executed in both *nix and windows systems.
//Do add 'cmd /C' to the start of $cmd if on a windows system.
$cmd = "echo '[start]';your commands here;echo '[end]'";
$output = user_exec($shell,$cmd);

fclose($shell);

function user_exec($shell,$cmd) {
  fwrite($shell,$cmd . "\n");
  $output = "";
  $start = false;
  $start_time = time();
  $max_time = 2; //time in seconds
  while(((time()-$start_time) < $max_time)) {
    $line = fgets($shell);
    if(!strstr($line,$cmd)) {
      if(preg_match('/\[start\]/',$line)) {
        $start = true;
      }elseif(preg_match('/\[end\]/',$line)) {
        return $output;
      }elseif($start){
        $output[] = $line;
      }
    }
  }
}

?>

[EDIT BY danbrown AT php DOT net: Contains a bugfix supplied by (jschwepp AT gmail DOT com) on 17-FEB-2010 to fix a typo in a function name.]