->Grober Unfug, Zossener Str.32-33, Subway-Station: Mehringdamm
Probably the best store in Berlin. Large selection of comics, books, merchandising etc. from all over the world. A whole lot of small-press-stuff and weird shit. Located in the south-end of Kreuzberg. Loads of coffee-places, record stores and boutiques around the corner on Bergmannstraße.
There is a german-language-store on the street-level and an international store upstairs. The place also hosts a little art-gallery. Check the website for their current show.
Grober Unfug
There is another smaller store under the same name at subway-station Weinmeisterstr./exit Schönhauser. They don't have the whole selection, but they will help you with your basic-needs too.

->Modern Graphics, Oranienstr.22, Subway-Station: Kottbusser Tor
The other big store. Large selection of US-stuff and German Independents. They also have interesting signings every once in a while. Located in the heart of Kreuzberg. Lots of bars and book-stores on the same street.
or Bundesallee 83, Subway-Station: Friedrich-Wilhelm-Paltz
The other store they have is a little further out in the west.
Modern Graphics

->That place in the backyard of the cinema Central called staalplaat(?) or somethign like that
It's in the back of the house which hosts the Cafe Central on Rosenthaler Str., Subway-Station : Hackescher Markt. If you follow the movie-posters into the last courtyard, go straight ahead, open the big metal-door and the store will be on the first floor.
They have all the avantgarde-comics and -design as you might have expected it from the description. Totally worth a visit and one of the most interesting backyards to visit in this crowded tourist-area.

->Peter Skodzik
Large store specializing in German comics and Action Figures. He has them all. A toy-collectors' wet dream!
Subway-Station: Nollendorfplatz. The store is on Nollendorfplatz 5 next to the theatre. Good Hot Dog-Stand with a good selection of vino on the corner and Winterfeldplatz just a block away. You'll find the reggae-bar Slumberland and a few other restaurants around here. Lots of gay-bars.

->Black Dog Comics
Specializing in US-comics. Big selection of Underground, including nasty xxx-titles.
Rodenbergstr. 9
blackdog

worthwhile visiting as well:

Renate-Comic Library
Hang-out for the local scene every first monday of the month.

Monday 14-20.00h
Wednesday 14-20.00h
Friday 14-19.00h
Tucholskystr. 32, Subway-Station: : U8 Rosenthaler Platz

Renate