As no-one else has risen to the challenge, I'll have a go!
First off, the really quaint small towns may not have a railway station, so you're likely to be limited to larger towns, like the places you've suggested.
I'm curious about the choice, as they are mostly mountainous - is this intentional, or would you like a contrasting area somewhere?
I don't know if you've already found it, but one really good resource for planning train trips around Europe is the *German* railways website reiseauskunft.bahn.de/bin/query.exe/en…
Checking this, your suggested journeys into Austria are likely to take quite a lot of time - somewhere between 8 and 10 hours for the trip from Annecy. My initial thought if you want a mountainous area outside France is the area near Interlaken in Switzerland, which has beautiful villages linked by an excellent transport network, which will take about 3 hours from Geneva.
I like Alsace, which also has its share of pretty villages, and Colmar is well worth a visit. However, the smaller tourist-magnet villages aren't accessible by train, so you'd need to investigate bikes, buses, organised trips, etc. http://www.ot-colmar.fr/
Looking for contrasts, there is Burgundy, particularly Beaune, which is worth a visit http://beaune.tctourisme.com/
And definite contrast, but not too far away, is Provence, staying somewhere like Aix, Avignon or Arles.
Well, you asked for suggestions!