Hi there: just back from the South Shore (aka The Lighthouse Route) myself. Others will chime in but my faves are:
Lunenburg: Trattoria della Nonna (great Italian using local seafood), Fleur de Sel (superior renditions of traditional and fusion utlizing all regional and organic specialities, great wine list)
Mahone Bay; The Biscuit Eater (cafe and book store with superb homemade sandwiches and such), LeHavre Bakery (excellent baked goods)
Halifax: Sushi Nami, FDS, Bish, Il Mercato, Da Maurizio etc, etc-really turning into a food mecca increasingly influenced by locavore movement, fueled by one of the best fresh markets on the eastern seaboard
There are a few previous posts that cover these two areas (but I don't think mention them by the "trail" name, so you might not have come across them). These might give you somewhere to start - or at least spark a bit of discussion on this very sleepy board. :)
A general impression is that there is a lot more on offer on the Lighthouse Route than on Marine Drive. However, Marine Drive is beautiful as an unspoiled look at coastal NS. LIghthouse Route is definitely on the more regular tourist route and so will have more restos and foodie stops.
Bring some BBQ from the City Market in Luling (the original, not the one in Houston) and I will dig some clams myself and meet you at the airport for an exchange!
I'm not too knowledgable about those areas, but I am certain others will respond. What communities are you visitng and when is your trip? Are you considering Cape Breton? The Cabot trail is simply not to be missed for anyone visiting NS.