There are lots of good coffee spots in Berlin, so it depends on the district you’re in. Most of my time I’m in Berlin-Mitte or Kreuzberg, so my selection (in an unpicked oder) would be: The Barn, Bonanza Coffee Heroes, Espresso Ambulanz, Oslo Kaffebar, Röststätte, Cuccuma, CK pour Voo.
P.S.: I totally forgot Godshot! Thanks, Benjamin.