If a process is reniced, then all its children inherit that niceness. So a PHP script can call proc_nice on itself, then invoke system(), and the command executed via system() will also be niced.
Also worth making a note of ionice. There's no PHP function for this, but it's important. A nice'd program will happily try to chew up all i/o bandwidth with very little CPU usage, it can therefore make the entire computer non-responsive despite the programmer's intention. Use "ionice -c3" or see "man ionice"