I've got all the three with suPHP, as well as somebody else has them with mod_ruid2. They say suPHP takes more resources, but I did not compare them. Note, I won't make a choice for you, it's up to you to decide what you want to get and what you want to use. And as I personally prefer suPHP (because of ability to use individual php.ini), I would persuade you to use suPHP.
What should mod_ruid2 to do with cli scripts since it's an Apache module? If you compile PHP with suhosin it really does not matter how do you use it: from command line or through mod_php/mod_ruid2, or via mod_suphp.