Since you are only going for two days, Versailles is kind of out of the question, because it pretty much takes a day. Goddamn is Versailles awesome.
If you've never been before, I'd recommend one day for the landmarks (Eiffel Tower, Notre Dame/Ile de la Cite, Arc de Triomphe/Champs Elysees, Place de la Concorde), and one day to just tool around the city. In particular, go to Montmartre and hit up at least the hill that Sacre Couer is on. Drink in a cafe and chill out. If you do go to the hill, go to the church entrance, but don't turn around until you get there. It's spectacular.
Also, since you are on short time, skip the Louvre/D'Orsee/Pompidou.