As explained in http://bugs.php.net/bug.php?id=39992, proc_terminate() leaves children of the child process running. In my application, these children often have infinite loops, so I need a sure way to kill processes created with proc_open(). When I call proc_terminate(), the /bin/sh process is killed, but the child with the infinite loop is left running. 
Until proc_terminate() gets fixed, I would not recommend using it. Instead, my solution is to:
1) call proc_get_status() to get the parent pid (ppid) of the process I want to kill. 
2) use ps to get all pids that have that ppid as their parent pid
3) use posix_kill() to send the SIGKILL (9) signal to each of those child pids
4) call proc_close() on process resource
<?php
$descriptorspec = array(
0 => array('pipe', 'r'), // stdin is a pipe that the child will read from
1 => array('pipe', 'w'), // stdout is a pipe that the child will write to
2 => array('pipe', 'w') // stderr is a pipe the child will write to
);
$process = proc_open('bad_program', $descriptorspec, $pipes);
if(!is_resource($process)) {
 throw new Exception('bad_program could not be started.');
}
//pass some input to the program
fwrite($pipes[0], $lots_of_data);
//close stdin. By closing stdin, the program should exit
//after it finishes processing the input
fclose($pipes[0]);
//do some other stuff ... the process will probably still be running
//if we check on it right away
$status = proc_get_status($process);
if($status['running'] == true) { //process ran too long, kill it
 //close all pipes that are still open
 fclose($pipes[1]); //stdout
 fclose($pipes[2]); //stderr
 //get the parent pid of the process we want to kill
 $ppid = $status['pid'];
 //use ps to get all the children of this process, and kill them
 $pids = preg_split('/\s+/', `ps -o pid --no-heading --ppid $ppid`);
 foreach($pids as $pid) {
 if(is_numeric($pid)) {
 echo "Killing $pid\n";
 posix_kill($pid, 9); //9 is the SIGKILL signal
 }
 }
 
 proc_close($process);
}
?>