The most common questions I get from travelers arriving in Cusco involve where to go for coffee or a drink or a bit to eat. Although I would not claim to know all or even most of the restaurants in Cusco, I definitely have some favorites! (look at my travel map for restaurant locations)
For Breakfast or Snack:
The Meeting Place: Delicious Waffles, Quality Bacon, Juices, Pastries and the best coffee in town. All profits go to local orphanages and ministry projects. Can life get any better? I submit that it can not (Brian Regan) On the San Blas Plaza.
El Buen Pastor: Decent coffee, but absolutely spectacular pastries. I´m talking chocolate croissants, peach and apple filled baked goods fresh out of the oven, and delicious donuts. On Cuesta San Blas.
La Bondiet: My favorite coffee shop in town. Mouthwatering cakes, cones filled with dulce de leche, small brownies, great smoothies, classy atmosphere, and great coffee! Located a block off the Plaza de Armas on Plateros and on the small plaza next to the Plaza de Armas.
Be brave and head to the markets. I personally find the San Pedro market a little dirty, but recommend heading to Garcilaso and the Wanchaq market for a bite to eat (walk away from Garcilaso until you get to the food stalls in the building). Ask for Sr. Jamie and try his Lomo Saltado or Arroz a la Cubana (S./7 and S./3) and try a juice from one of the ladies opposite his stall!
Jack´s: alternatively, try the lonely guide / rough guide favorite at the bottom of Cuesta San Blas for big and late breakfasts (El grande), gourment sandwhiches, and soups like Tuscan vegetable or pumpkin that make your mouth water (my Mom went 3 times in 9 days! That says something for the quality of their food).
Olas Bravas: Ceviche is excusively a lunch food, and Olas Bravas on Mariscal Gamara near the start of Av. La Cultura does it well. Try the Jalea, the Lomo Saltado con Tacu Tacu, and the Ceviche Mixto (warning, huge portions).
I think I could eat at a different restaurant every night in Cusco and still have thousands to try. Some of my highlights have been fusion cuisines near the town center.
Cicciolina: Located a block off the Plaza de Armas on Truinfo (second floor). Absolutely incredible tapas, wine list, and the best Pisco sour that I have had in Cusco. (U.S. prices and reservations suggested in high season).
Two Nations: An Australian / Peruvian fusion restaurant a few blocks off the plaza that has a giant burger, good soups, and solid Peruvian cuisine. Walls decorated by happy diners.
Los Perros: Two blocks off the plaza. And makes this list because it is the home of one of the most delicious burgers I have had (and one of the largest) with great potato skins, and other sides.
Some shout outs: Paddy´s (corner on the plaza, good quesadillas and wings), Real McCoy (for some real British cuisine on Plateros), and Numa Raysi (Triunfo for some real good, real authentic Peruvian cuisine!)