Arguably two of the best: Samadhi in Mitte ( http://samadhi-vegetarian.de/samadhi/live/index_en.html ) and Lon Men in Kreuzberg ( Großbeerenstraße 57 a).
Also good is the Cafe V, but they serve also fish dishes (Lausitzer Platz 12, also Kreuzberg).
Sort of a fast food vegetarian restaurant is the yellow sunshine (Wiener Str. 19, also Kreuzberg, website, only in german: http://yellow-sunshine.de/ ) with vegetarian burgers and similar stuff.
A totally vegan restaurant is Maja's Deli in Prenzlauer Berg, but never been there. (Pappellallee 11, Metro/U-Bahn Eberswalder Str.)
Additionally you can order a lot of vegeterian dishes in nearly every vietnamese/Thai/japanese restaurant of which there are a lot in Berlin.