We had a truly excellent dinner the other night at La Truffière in the 5th near Rue Mouffetard. An excellent menu of French classics with some emphasis on truffles, but good broad coverage. The room was great, the staff was friendly, an amazing wine list, everything that goes into a comfortable dinner. Often hard to find in combination in Paris!
The one drawback is the place is very expensive. 110€ per person for the big tasting menu, and precious few bottles under 100€. (Note: this is much higher than listed on the web site. Hmm.) The non-smoking room was about half Japanese tourists and only one French table, I suspect their prices generally keep the locals away. Still, we had a perfect meal, so money well spent.