We just returned from Rome.

Armando al Pantheon - Our second visit. Excellent with interesting wine list. Reservations open on the restaurant's website 30 days prior and book almost immediately for dinner. Stanley Tucci featured it on Searching for Italy, which added to its notoriety.
Colline Emiliane - Fantastic, features dishes of Emilia Romagna. Best homemade pasta of our trip. Book ahead, great for Sunday lunch.
Piatto Romano - Located in Testaccio and specializes in "cucina romana." Great for offal and game lovers, but plenty of pasta dishes.
Salumeria con Cucina Roscioli - Casual (you're seated in the store), where platters of prosciutto/mozzarella and other antipasti are prepared. Solid pastas and other creative offerings. Reservations are essential.