Ouigo (train)
Ouigo is a low-cost train service offering tickets departing from non-major train stations. Official website here.
Blablacar (car sharing)
Blablacar.fr allows users to find car sharing rides (or propose some). Pretty popular among French people, it is mostly useful for short (~400km max) distances, after that it becomes pretty expensive compared to the other options.
Each driver has a profile with some information and reviews.
Ouibus
Ouibus offers cheap and comfortable (toilets, wifi) bus rides. Even offers destinations outside France. Offical website here.