Leigh, I found the older churches of Paris to be very different than those of, say, Italy, Germany, Belgium, etc. Almost all of them were stripped of their interior decorative accoutrements and abused during the Revolution so they felt a little bare but have value nonetheless for their architecture and histories.
Where interiors go, Sainte-Chapelle should definitely be top of list: the windows alone in that one will blow your mind.
The exterior of Notre Dame was more captivating, IMHO, than the interior. Same for the Sacre-Coeur, which I agree can be skipped if there isn't time. Nearby Montmartre cemetery was more interesting than the church.
I'll agree with Anita on Église Saint-Sulpice: that one has some Delacroix frescoes, an interesting gnomon, and one of the largest organs in the world. Also with Nancy on La Madeleine: not originally designed to be a church at all but has a lovely altar.
Will echo SharYn on Saint-Étienne-du-Mont (St. Stephen), Add that to the list for a look at its lacy, 16th-century double-spiral rood loft - said to be the only surviving screen in Paris - and shrine of the city's patroness, Geneviève: her bones largely destroyed during the Revolution but the base of her sarcophagus and scant remaining relic encased in gilded reliquaries.