I can recommend Honigmond
Address: Borsigstrasse 28. Underground: U6 Zinnowitzer Strasse.
"This quiet, neighbourhood place serves up traditional German food alongside a bi-weekly menu of innovative dishes ranging from kangaroo to Swiss fondue. Not to be missed are the Konigsberger Klopse (East Prussian meatballs in a creamy caper sauce) and the best Caesar salad in town. If the decor is somewhat short of the 1920's nostalgia it tries to evoke, the excellent small wine list and remarkable home-made bread make up for it."
I've recommended it to lots of people who all loved it.
Also in Prenslauer Berg:
Gugelhof
Knaackstrasse 37, Underground U2 Senefelderplatz
Tel 442 9229
"This is the place where Gerhard Schroder took Bill Clinton. He probably took one look at Bill and decided the fromer president would like something filling but with a touch of refinement - and that's just what you get at this Alsation restaurant that pretty much pioneered the Kollwitzplatz scene in the 1990's. The choucroute sonctains the best charcuterie in town, and the backofe (meat and potatoes with root vegetables) uses superb riesling subtly to underpin its simplicity. Reservations a must"
This had a great atmosphere too but was more expensive.
Both from Time Out Guide which I recommend too.