What is a good argument against Aquinas' 'Five Ways'?

You ought to read David Hume's Dialogues on Natural Religion. Aquinas presents five arguments for God ("five ways"). Which have you in mind?

It would help the discussion if a reference to the appropriate questions in the Summa were provided, or at the very least a brief outline-list were to be provided so everyone could understand the question.

An atheist would object to Aquinas' view by saying just because something looks like it was created a certain way, and looks like there is a God behind it is not the same as proof there was a God behind it because we didn't see God create the universe, so if we didn't see it in action you can only guess to how it was done.