There are various sites with restaurants reviews, for example those in our list of other relevant websites. What you'll find below, are our personal recommendations.
In order to help you stay focused, we tried to limit ourselves in each category to 4-7 places. Not all websites have an English version, so if you're puzzled and can't figure out the address etc., we'd be happy to help.
Please also note that none of the these restaurants is certified as kosher, for kosher restaurants, please have a look at the page Eating Kosher in Berlin.
And last but not least, here's an interesting article about tipping in restaurants.
Schnitzelei: The name says it all... But except for quite a few different kinds of Schnitzel, they also serve “German Tapas”. They have two locations, one in East-Berlin and the other in West-Berlin
Charlotte & Fritz: Located at the Regent, one of Berlin's finest hotels at Gendarmenmarkt, this very continental restaurant isn't as expensive as one might expect:
Augustiner: a piece of Bavaria in Berlin, lots of authentic pork dishes, but also a very delicious beef goulash with Spätzle
http://www.augustiner-braeu-berlin.de/
Braufactum: Everything you (n)ever wanted to know about German sausages - and beer!
http://www.braufactum-hausvogteiplatz.de/
Kartoffelkeller: Berlin's "Potato Cellar" has a very local atmosphere and clientèle, and although it's located very centrally, hardly any tourists go there:
https://www.kartoffelkeller.com/cms/index.php/de/
(irrelevant in wintertime, naturally)
Café am neuen See: very nicely located next to a lake within the Tiergarten (Berlin's "Central Park"), fantastic ambience on Summer evenings
http://www.cafe-am-neuen-see.de/
Prater: Berlin's oldest and largest beer garden + restaurant
Golgatha: Not as deadly as it sounds...
http://www.golgatha-berlin.de/
Strandbar Mitte: Not exactly a beer garden, but really nice + very close to the famous Museum Island you'll surely visit
http://www.strandbar-mitte.de/strandbar/index.html
Gasthaus Alt Wien: "Old Vienna" is in the posh borough of Prenzlauer Berg and seems to have the quality to stick around for many years
Ottenthal: An honorable establishment in Berlin's bourgeois quarter. If the TV series "Mad Men" had taken place in Berlin, this would definitely be one of their dinner locations
Austria: The largest Viennese Schnitzel in Kreuzberg, I recommend sharing one for two... Please note that there's another place, called "Felix Austria", which you might see on your way looking for the original "Austria" - this recommendation refers to the original that's simply called "Austria"
Jolesch: Combination of traditional Austrian cuisine with some modern interpretations in a trendy but cosy atmosphere
Knödelwirtschaft: All about Austrian dumplings in two different locations (North and South)
https://www.knoedelwirtschaft.de
Seaside: Located at the very center, close to Gendarmenmarkt, a seafood bar with an urban atmosphere
http://www.seaside-fish.com/en/
Der Fischladen: a popular and, in the positive sense of the word, simple place, which is really all about freshness
Munch's Hus: a little piece of Norway in Berlin, including some fantastic grilled salmon
The KaDeWe: Germany's largest department store dedicates two floors just for food, including several very fine bar-restaurants for fish, oysters and lobsters in its 6th floor, where you can sit around the kitchen and watch them preparing your food
http://www.kadewe.de/de/gourmet/bars_restaurants/
Bocca di Bacco: probably the best (and most expensive) Italian in Berlin
The 12 Apostels: a classical choice with 2 great locations
Mondo Pazzo: very popular with locals
Il Pane e le Rose: in Berlin's trendy Friedrichshain quarter of the young & beautiful
No website; address: Am Friedrichshain 6, 10407 Berlin. Tel.: 030-4231916
I Due Forni: Probably the most Mediterranean atmosphere that a Berlin pizzeria can offer
No website; address: Schönhauser Allee 12, 10119 Berlin. Tel.: 030-44017333
Pasternak: Russian delicacies in one of Prenzlauer Berg's most beautiful streets (it's really close to the Rykestraße Synagogue and, although not kosher, offers sometimes Russian-Jewish specialties)
http://restaurant-pasternak.de/
Gugelhof: Let me put it this way - when I (Yoav) was studying in Heidelberg, my German professor for philosophy asked the class, where the best German cuisine is. Everybody said something, but at the end he corrected us all and answered: The best German food is in Alsace (which is, nowadays, actually a part of France, although many Germans still consider that as an unofficial part of Germany). So, to put it short, Gugelhof serves Alsacian food at its best.
Breslau: Polish "Pierogi" and much more from Eastern Europe's most fascinating land (in Yoav's eyes)
https://www.restaurantbreslau.de
Baba Angora: Germany and especially Berlin has a big Turkish community and while most tourists try Döner at some point, the Anatolian cuisine has a lot more to offer.
Faro: Authentic Spanish Tapas, Paella and more
Tibet House: really cheap, really tasty + different than Indian/Chinese food
No website; address: Zossener Straße 19, 10961 Berlin
Monsieur Vuong: very trendy, very Vietnamese
Sasaya: the Japanese for an easy evening
Dae Mon: Very fine Korean/Japanese/European fusion (“open minded”) cuisine
Transit: Thai and Indonesian delicacies in two different locations (Mitte and Friedrichhain):
http://www.transit-restaurants.com/
Two Buddhas: Asian with a twist, in a historical, protected building at relatively central location
http://www.nordbahnhof-two-buddhas.de/eng/restaurant.html
Kuchi: interesting sushi creations at different locations (East + West Berlin)
Cookies Cream: very stylish, very trendy, very veggie
Frea: Berlin's first vegan zero-waste restaurant, fine-dining with a good conscience
Momos: vegetarian dumplings in a simple, nice eatery
Lucky Leek: Your best choice for a stylish vegan evening in the (stylish, of course) borough of Prenzlauer Berg
Umi Vegan: Plant-based, organic Japanese food not far from the Kurfürstendamm Avenue
Soy: Great vegan Vietnamese food, very centrally located
Entrecôte: French cuisine meat, passionately devoured by Germany's politicians
Grill Royal: where Berlin's VIPs meet for meat, usually a well massaged Kobe steak
Tony Roma's: very American ribs etc. Could be interesting for guests who don't come from the US...
http://www.tonyromas.de/index.php?id=58
The Bird: great steaks, but quite often crowded, so don't forget to make a reservation
http://www.thebirdinberlin.com/
Balthazar: French style
http://www.balthazar-spreeufer.de/
Steakhouse Asador: Reasonably priced and yet not as touristic as the large chains ("Blockhouse", "Maredo")
http://www.restaurant-asador.de/
Rausch Schokoladenhaus: Berlin's oldest chocolate house, est. 1863, and as they maintain, the world's largest. There's a shop, and on the second floor a very nice café with all kinds of chocolate creations...
https://www.rausch.de/schokoladenhaus
Sawade: Just a bit younger than Rausch, but some say better, Sawade is a local establishment for handcrafted chocolate art works. One of their locations is in the famous Hackesche courtyards, which is right within the so-called Jewish quarter
Martin's Place: Joseph Martin is an Israeli chef that makes the most delicious cakes in Berlin's multicultural and multi-ethnic borough of Neukölln
Der Kuchenladen: The "Cake Shop" is, well, exactly what it should be. Great cakes that go well with an afternoon tea in West-Berlin's very bourgeois borough of Charlottenburg.
Ritter Sport's World of Chocolate: Except for the huge variety of products, they offer children the opportunity to make some chocolate themselves. Adults can make up their own recipe and let the professionals prepare it. Why leave Berlin with a normal souvenir when you can bring your very own kind of chocolate as a great gift for your loved ones back home?
http://www.ritter-sport.us/#/en_US/berlin/
(not including kosher places)
Zula: Humus by candlelight in the stylish borough of Prenzlauer Berg
Yafo: Sophisticated Tel-Aviv kitchen in Mitte (close to the Jewish quarter)
Kanaan: a Jewish-Arab joint venture, inexpensive, with some Yemenite touches
https://www.kanaan-berlin.de/de
Doda's Deli: Soul-food, just like you favourite Israeli aunt would cook for you in the trendy borough of Friedrichshain
Beba: Fusion of Jewish cuisine from all over the world inside the Gropius-building, great brunch on Sundays
https://beba-berlin.com/restaurant/
Feinberg's: Very popular with locals, close to the KaDeWe
https://www.feinbergs.de/en/home
Lorenz Adlon Esszimmer (= dining room): Located in Berlin's most famous hotel, the Adlon, overlooking Brandenburg gate (come early to get a good table at one of the windows!)
http://www.lorenzadlon-esszimmer.de/
Prism: By the Israeli chef Gal ben Moshe
Tim Raue: Unlike most other gourmet restaurant, the German chef Raue chose a somewhat different location for his double-starred restaurant, namely the multi-cultured borough of Kreuzberg, and as you might expect, his menu includes interpretations of different, international cuisines
http://tim-raue.com/index.php?task=restaurant§ion=aktuelles&lang=en
Horvàth: Under this Hungarian name, Austrian-born chef Sebastian Frank gives his special "Austro-Hungarian" touch to this restaurant, which has been starred in many guidebooks
http://www.restaurant-horvath.de
Rutz: The only restaurant in Berlin with three Michelin stars
https://rutz-restaurant.de/en/
(primarily because we didn't think of a better title yet)
Lokal: The website's not very impressive, but nevertheless, it is usually booked long in advance
http://www.lokal-berlin.blogspot.de/
Katz Orange: Great ambience, exotic food creations (really)
Layla: Mediterranean & Middle-Eastern fusion cuisine by Israeli star chef Meir Adoni
https://www.layla-restaurant.com/
Amigo Cohen: Israeli-Mexican fusion
http://www.amanogroup.de/en/eat-drink/mani-restaurant/
Michelberger (within the Michelberger hotel): Organic, local and “communal” dining (you and the people you're dining with are supposed to share each dish)
http://michelbergerhotel.com/en/restaurant
Neni: tasty Israeli cuisine with a spectacular view of the city