I like backbar in Zurich-Seefeld, they also have very nice bread, fresh salad, juice & co., Felix & Odeon at the Bellevue are tradional but interesting coffee shops
spheres, kafi für dich, kafischnaps, myplace, z am park, cafe des amis, bürgli, grieder, cafe zum guten glück, tearoom, bebek, wohnzimmerbar, dieni muetter, casablanca, gloria... its simply too many to list...
Cafe des Amis has my favorite big cup of coffee. When I moved here it was an adjustment to having such small cups of coffee, but cafe des amis has a big milchkaffee that is very, very good.
I also like Maison Blunt in the summer, they do an iced coffee, as does Spheres and Henrici.
Henrici's iced coffee was good but seriously tiny.