Japan (or so I would like to think) in the middle of Brooklyn, NY

Zenkichi (www.zenkichi.com). This place is literally a hidden gem. Modern Japanese cuisine coupled with amazingly calm and balanced atmosphere and beautiful design. You will not find this place unless you are actually looking for it. No signs welcoming pedestrians, no flashy ads, nothing. Just a wooden wall and a door. Come in. Once inside you will find several levels of very private booths, in which you can only see your party. It is quite interesting to be able to hear silent voices around you but not to see anybody. This is the kind of place that makes you automatically want to silence or switch off your phone. They do not allow children under 14 to maintain this sense of calm and subtle beauty. 

The food is fresh, unusual and shows that Japanese food is not all sushi. The flavors are subtle and fragrant, the methods of cooking bring out the natural tastes of each ingredient, without overpowering with sauces or spices.  The tasting menu is a great choice, especially for those unfamiliar with the cuisine and the menu. The sake menu is very extensive and well selected. 

Should I return to New York in the near future, I will definitely come back. Excellent place.

Photo (c) www.nydailynews.com

City View Dim Sum

Located on the threshold of FiDi and Chinatown this restaurant has a little bit of both. It serves fresh tasty dim sum for prices that are to be expected for its location - more expensive than in deep dark Chinatown but not as expensive as the Financial District crowd often is willing to pay. While you will get the same quality for less money in a small, grungy place where the only way you are going to get your food is if you order in Cantonese, City View is a good option for a sit-down lunch. It's clean, comfortable and the staff speaks some English - enough to explain which dumplings have shrimp and which ones have pork.
You never know how much your bill will be - the waitresses walk around with little carts, on which you can find all kinds of delicacies. Once you choose something, they mark your tab with a stamp, but you will never see prices anywhere. On average the bill ends up somewhere around $25 per person (free tea included, or do they charge for it? Who knows.)

Compared to the Oriental Pearl on Clay St, these guys do a much better job for the same price. And I kind of like the idea of choosing from a variety on a cart rather than choosing in advance from a menu.

They are only open daily, 11:00 AM to 2:30 PM. Cards accepted.

Photo (c) - yelp.com

Tokyo Fish Market

Hands down the best place for fresh fish and Japanese groceries in Berkeley. After buying fish from Berkeley Bowl for a long time, I switched to this little place and am highly impressed - clean and well-organized facilities, excellent fish and seafood and very friendly service (they will scale, clean and cut the fish for you in any shape of form). They have a wide selection of sushi-grade fish and an abundance of other ingredients.
Price-wise it compares to any other fish section of a major grocery store.

Their gift shop is full of nice little treasures like cast-iron tea pots, mugs, ceramic ginger graters and flip-flop socks.

They are open Mon. - Sat. until 6PM.

Photo (c) - yelp.com

Amanda's

Amanda's is a new "fast and healthy food" restaurant in Berkeley. They serve quick meals and snacks that are fresh, affordable and healthy (as healthy as burgers can naturally be).
The location is a bit questionable since it's right next to the BART station and this area was never able to keep decent food places around long enough. However, the menu sounds promising with apple fries with a honey-yogurt dipping sauce, sweet potato fries, a number of fresh salads and home-made ginger ale. They also use 100% compostable packaging and utensils.
The menu is limited but with a theme throughout, which, according to Gordon Ramsay, is the way to go in the restaurant business.

Open until 9 PM, it is a good option for lunch or for a light dinner.

Photo (c) - yelp.com
www.amandas.com

Close and Far - the beginning

This will eventually become a very subjective guide of nice places to explore and good food to try.