A few personal favorites (I’ll try to keep the list updated)
Restaurant 3 - somewhat under the radar, simple and stylish, modern italian fare (my personal favorite in Berlin, highly recommended)
Cafe Einstein (breakfast) - A return to cafe house culture. International newspapers. Good breakfast. Two locations (the old one is better).
Bar Buck & Breck (brunnenstr 177) - the best cocktail bar (in the world, maybe). tiny and hard to find. ring the door bell! when they are full, they are full (no waiting list). don’t go with more than 2 (max 3 people).
Cookies & Cream - expensive stylish vegetarian restaurant, that is attached to a house club. great location, and if you go on a club night, you can enter the party straight from the restaurant, skipping the line and bouncer.
Bonanza Coffee Roasters - my favorite of the hipster coffee shops. These guys were the first, and they are still the best and nicest. I hate their competitors The Barn.