1) Marche aux Puces des Clingincourt is so great. You can seriously stay for hours, great little finds. Lunch place here is called Chez Louisette and they sing to you during your meal and its CLASSIC. Was recommended first by a friend of my sisy's Jenny who has a cute new blog http://www.velvetfoxtail.com/. All the designers love Chez Louisette and go here religiously!! Its located directly inside the market amongst all of the little venders, but if u ask someone inside they'll be able to tell u. The moules are really good, and the smoked salmon. Apparently the salads are a no go. http://www.discoverfrance.net/France/Paris/Shopping/Paris_fleamkts2.shtml#
2) Marché d'Aligre- This is where all the serious dealers go when on the hunt for original antiquities from across the country! Some of the cheapest prices in Paris, particularly the further away from the St. Antoine side you get. I found some great little antique books for 5 euros, old ballerina slippers, a hat and the most amazing looking strawberries, mangos and fresh flowers! http://marchedaligre.free.fr/
3) L'Annexe des Créateurs-Ok not antiques per se but one of the best second hand clothing in my opinion.