We just wandered around St. Tropez on our own, looking in shops, walking up and down and around the little alleys and along the waterfront. My husband climbed all the way up to and went thru the Citadel. We had lunch and a restaurant along the waterfront while ooogoling all the fantastic yachts in the harbor and spotted George Hamilton right in front of us. Its just a really pretty, charming and delightful town.
In Marseille we took the Aix en Provence tour, so didn't see much of Marseille. Next time though we would definitely just wander around on our own and maybe stop for some bouillibase along the waterfront and such.
Haven't been to Bonifacio, so no help there.