Cafe Eucalyptus
Very popular with travelers, they offer everything from Pad Thai to pasta, salads, hummus and guacamole, all very tasty. It's warm and friendly, and also good for groups. Quite expensive for Ecuador, $5.07 for a coca-cola plus tip makes one think that the travellers are taken advantage of.
La Fornace is the best pizza place in Cuenca and has three or four branches there. The fruit pizza is excellent and quite inexpensive. The ice cream there is also delicious and costs about 70¢ for the first scoop.Some of the "hole in the wall" diners and eateries can be surprisingly good. There's a small restaurant located between two shops on the main plaza, where they serve wonderful chicken with vegetables.
Women's Coop
Cheap, nutricious, and local lunch with a soup and a drink. Made by indigenous women in a sweet courtyard. Vegetarian and meat options.