If you love cheese Fondue, you’ll love Ars Vini. This Swiss restaurant has 3 branches in Berlin: in Mitte, Prenzlauer Berg and Charlottenburg.
I can’t tell which one is the best, in all venues, a very friendly staff will warmly welcome you. The choice of cheese fondues is very wide in winter, more restricted in summer, but there are also meat, fish and vegetable fondues in which you dip your food in oil or bouillon, as you wish. Meat is usually very good quality, but I personnally prefer having cheese fondue. The Schweizer Klassiker, traditionnal Swiss, is a delight. I also enjoy a lot the Österreisches Fondue with diced bacon in it, delicious! Other fondues are also a hit.
As for wine, the waiters will give you recommendations and offer you to taste a couple so you can choose the one you like the best.
Pricewise, it’s quite cheap for the high quality you get, no ripp off, great food, friendly staff, cosy athmosphere, 3 very good spots indeed.
EDIT April 2016: Since I first wrote this article there has been some changes and only the location in Prenzlauer Berg remains, still worth a visit.