I can wholeheartedly recommend the Nostress restaurant/cafe just off of the Old Town Square at 9 V Kolkoven, Prague 1. It looks like a breakfast place or coffee shop from the outside, but had a very inexpensive pris fixe menu at lunch and a more extensive menu at dinner. The food is excellent & the desserts are to-die-for. My husband says that if this restaurant were in our neighborhood in Boston we would eat there once a week. www.nostress.cz Facebook.com/nostress.cz
We also liked the Address Idea Kitchen ramen bar at 28 Rinja - very good ramen in a techno/grunge atmosphere (www.kitchen-ramen-bar.cz) and George Prime Burger, 32 Vodickova (georgeprimeburger.com/cs/). Just burgers, but really good ones.