Show step-by-step dialogs for helping user with using the site
The modules chrischarlton suggested were fine, but those are unsupported and not maintained.

I recommend using the Boostrap tour module. With this module, you can show popups step-by-step, attach the popups to HTML elements in each step, save the progress of the user, and let the user add feedback to the tour. However, you need to have a boostrap based theme in order to make it work.