'I'm thinking of Annecy for 4 nights (with a couple of day trips: Geneva? Chambery?), but we prefer small places with fewer crowds'

We spent one night in Annecy after Chamonix & Val D'Aosta. We were very disappointed...did not find Annecy charming primarily because it is overrun by tourists. A little better in the evening but restaurants are packed and service terrible (generalizing a bit but this is typical of a place that is too touristy). One of the only places that left me feeling underwhelmed in our almost 2 week trip that covered Alsace and the mountains.

Based on your statement about crowds I would recommend you stay elsewhere. We drove around the lake and found Tallories small but a lot more charming.

All Valleys West of Turin are fine for hiking, but it's absolutely necessary to check where are open hotels and open restaurants. Some areas are really isolated and scarcely inhabited.
The Sestriere-Bardonnechia-Oulx area is more touristy. So is the area around Limone Piemonte and - in a certain mesure - Val Roya, between Limone and Ventimiglia.

You trip sounds lovely-we did something similar in June/July of this year.

I agree with previous posters about Annecy. We spent 3 days there this summer and it was far more touristy than we were expecting. However we made the most of it-rode bikes around much of the perimeter of the lake followed by a wonderful relaxing swim in the lake and lounging in one of the free public beach areas, and took a day and drove up to the Semnoz Pass for some lovely views and hikes. I would suggest if you stay in that area you explore outside of the city for best outdoor activities.
We did stay in a nice apartment with a lovely hostess in Annecy, and there was an absolutely fantastic patisserie across the street. But otherwise the food was not at all good (and we were quite selective).
We love Liguria and we also loved our time in Lyon during this last trip. We kayaked in a cove between Portofino and Santa Margherita Ligure and it was spectacular, the food in Liguria is outstanding, and have had lovely times in both Sestri Levante and Portovenere. Lyon was really a beautiful and accessible city and we wish we had stayed longer than three days.

We also did four days in Cogne-the hiking is just spectacular there. We parked our car at the hotel and explored every day and evening on foot without a problem, as there are lovely trails all around to the surrounding towns and into the National Park. The hiking map was well worth the 5 euros! And Chamonix was also fantastic, as was a town called Champoluc.

Enjoy your trip...it was a wonderful time to visit.

Thank you all so much for all your help. Rather than Talloires, would you recommend somewhere near Aix-les-Bains as a base for day trips to Annecy, Chambery and perhaps Lyon?

don't worry! Talloires is about 10 miles from Ugine from where you can easily reach Chambery and Lyon on a motorway. Other motorways go from Annecy to Chambery - Lyon and to Chamonix.

Thanks so much, neckervd! I'd really like some advice about moving our Haute Savoie/Rhone base from the Annecy/Talloires area to somewhere a little further east - closer to Lyons. We then have to drive back into Italy, so I'm trying to avoid going too far west (or north or south) of Lyon, but I'd love somewhere closer to the Beaujolais area than we currently are.
My logic is this: we'll already have had more than 2 weeks in various mountainous areas (Cogne, then Courmayeur, then Chamonix): we'd like to experience more of the gracious towns and historic villages of eastern France, rather than stay somewhere where the main attraction seems to be the proximity to the mountains.