Pearl Restaurant and Oyster Bar is in my opinion the best restaurant currently in Peterborough. Cuisine is Asian/Fusion and Oysters. Can be noisy and the tables are close together because the space is small. It's not open on Sundays. http://www.pearl-peterborough.com/
Harlow's Pub is casual pub food with a good selection of sandwiches, soups, salads, beers. Service can be painfully slow sometimes. Also closed on Sundays. http://harlowspub.com/
Lee and Mt. Fuji and the Boilerhouse has decent Chinese/Japanese/Sushi http://leeandmtfujiatboilerhouse.com/
There are two relatively new restaurants in downtown P'boro which I have not been to yet, but perhaps someone else can weigh in on: Waterhouse Restaurant in the old Acqua Bistro space http://www.waterhouse-nh.com/ and new italian restaurant (name escapes me) where Gatto's/Intermezzo/Old Theater restaurants used to be.