What is the ruling on money taken by a son from his father, who was employed by him, without his knowledge? And is it considered part of his wages or a debt owed by the deceased father?

If what you took from your father's money is equivalent to your unpaid wages, which you did not waive, then there is nothing against you. This is what scholars call the issue of "al-Dhafr" (taking one's due by force). Some scholars have supported this view, citing the Almighty's saying: (Then punish with the like of that with which you were punished) and (So transgress against him in like manner as he transgressed against you). If you took more than your wages, then you must return the excess to his inheritance. It is not permissible to give it away as charity except in case of inability to reach him or his heirs.