When resolving a spell or ability you need to follow the instructions in the order written.  This matters for some spells like the Primal Command from Lorwyn.  If you choose the second and third modes and target a noncreature permanent owned by the targeted player, then that player will put the targeted card on top of his library and end up then shuffling it into the library.  Got any other situations or spells where the order they resolve in matters?  Feel free to share them in the comments.