Small towns Southern France

The closest towns to San Sebastian, accross the border in the French Basque Pyrenees, that are accessible by train, would be St. Jean de Luz and Hendaye. I have never visited Hendaye, so I really can't make recommendations, one way or the other. St. Jean de Luz is a very nice, traditionally basque town. Though it was once a major basque fishing village, tourism has now taken over as it's major industry and fishing had taken a back seat. While I am not sure I would call it "quaint", I would recommend it and have always enjoyed my visits there.

The only other towns on the French side of the Basque pyrenees that are accessible by train (that I am aware of) are Pau, Bayonne, Biarritz, St. Jean-Pied-de-Port, and Oloron-St.Marie. Pau and Bayonne are both fairly large, busy towns. Biarritz is a resort town and definitely not quaint. St. Jean-Pied-de-Port is a beautiful basque town. It is also one of the starting points of the pilgrimage to Santiago de Compostela in Spain, so it can be crowded with tourist. But none-the-less well worth a visit. Of all, the quietest and most "off-the-beaten path" would be Oloron-St. Marie. For an overnight visit, I would think it might be a little to far out of your way.

Long story short, I would recommend St. Jean de Luz.

I agree with Linda....St. Jean de Luz would make a great night-time stop, and its on the route most of the daytime trains take from Paris to San Sebastian.
Hendaye is nothing to write home about....an interesting "canal" and a couple of nice old churches...and they've spend a lot of money sprucing the place up. Not much "atmosphere" there, but it is a place you won't find many tourists! ;)

I would also like to vote for St. Jean de Luz. I really enjoyed there little harbor protected beach front. The entire town can be done on foot and you can enjoy the little harbor ferries and the historic church. Check Rick's book for a lot of good info on this town.