I'm not sure what you mean by "program," so I'll address both possibilities:
If you're thinking of web scripts (i.e., a PHP script that is served by a web server), then you would use the include() or require() directive -- check php.net for more information on the difference between those. In either case, you can access the variables in the "called" (i.e., included) script as local variables. That is:
//foo.php:
print $foo;
//bar.php
$foo = "Hello, world!";
require("foo.php");
would print "Hello, world!"
However, if you are writing scripts for execution on your local system (that is, perl-style) or using PHP-GTK, and you want to execute another similar script, then I would use any of the various commands and operators PHP has for such a thing, depending on what you want to do with the output. Check out the passthru(), system(), and shell_exec() commands, as well as the `` (backtick, not single-quotes) operator. With these, you can do something like
$output = `chmod -R 0700 *`;
And just put in any command there, with command-line arguments that would become your PHP script vars. Now, I don't have much (read: any) experience with this, so this is fairly conjectural, but I'd bet dollars to dimes it would work.
That help?