We are presently in Bayonne via train. We want to eventually get to Lyon. It appears we should overnight at least one night somewhere in between. Looks like the train goes through Toulouse, Montpellier and Marseilles. We have not been to any of those. Does anyone have preferences of which town and any lodging suggestions??
I'd be very surprised if you really can't get from Bayonne to Lyon by train in one day - check the schedules at voyages-sncf.com or bahn.de.
If you think the trip is too long for one leg, all the places you mention have points of interest. I've never been to Toulouse, but it's meant to be nice. Montpellier is a relatively low-key town with a pleasant old centre and some nice restaurants. Marseille is roughly the third biggest city in France and the "grittiest" of the three, but it's fine if you have at least a basic sense of urban self-preservation and has some very atmospheric sights (most of the crime rate that hits headlines is gangsters killing each other over gangster stuff, not a threat to visitors).
I can't speak for the train schedule, and I have not been to any of the cities mentioned, but based on my present "research" for an upcoming trip, i'd vote for Marseilles, as it has the port activity and enough interest for an overnight. I checked the distance from the train station to the port area , it looks like a 10 min walk, and there are a bunch of hotels in the area under $ 90 / nite., including an ibis. Looks very do-able if you don't have a ton of luggage.
The train route on Rome2Rio website shows Bayonne>Toulouse >Montpellier > Lyon. I've visited Toulouse and it's a very pleasant city with some interesting museums as well as river and canal cruises. The TI has maps with a number of interesting walking tours. And the cassoulet at Le Colombier restaurant is outstanding. Here's a link to the city's tourism website.
I've never visited Montpellier but have been to Marseille twice. Yes it's a gritty city but one of my favorites because of its unique multi-cultural heritage.
I've been to all three and agree with the Toulouse suggestion for all the reasons stated. Montpellier is second choice. Marseille needs more time for probing.
The schedule links mentioned by the first Phillip/UK are more accurate than Rome2Rio in showing all the options. If you leave at 8:00 a.m., you can make the trip in 8 hours with connections at Toulouse and Nimes. If you leave at noon, you can make it with just one connection at Toulouse, arriving to Lyon at 22:00.