Berlin im Untergrund - Play with toys promoting an (amazing) interactive CD related to the world under Berlin (in German).
Berliner Bunkernetzwerk - A databank of subterranean military leftovers around Berlin (in German; English mirror broken).
Berliner Unterwerten e.V. - The society for the exploration and documentation of architecture under Berlin (in German, with a passable English mirror).
Bunker-Anlagen - Photo-oriented tours of military leftovers, primarily bunkers (in German).
Bunkerland - Bunkers and military leftovers under Prussia (in German).
Dubtown Industriekultur - Great-looking site of industrial ruins in Germany, with lots of impressive pictures (in German or English).
Eisenbahnrelikte.de - Abandoned railways and railroad stations across Germany (in German).
Industrial Archaelogy and Cultural Landscape - Some very impressive pictures of abandoned buildings and rooftops (mostly in German).
Ostwall.com - History of, and excursions into, an abandoned system of fortresses and tunnels (in German).
Relikte - Maps, plans, descriptions and some incredible photos of military leftovers in Bremen and Lower Saxony (in German).
Shedworks - Pictures of women who, for some reason, enjoy hanging around in abandoned buildings naked (in German with some English).
Shelter Team - Site of a group of explorers probing underground buildings (in German; currently down, hopefully temporarily).
Stahl Art - Breathtaking, arty pictures of historic industrial architecture in Germany and beyond (in German or English).
Spuren der Industrie - Photos of abandoned factories, breweries and mining operations in Germany (in German).
Third Reich in Ruins - Although more academic than adventurous, this site offers a collection of maps, pictures and snippets of trivia useful to those seeking military leftovers in Germany (in English).
Undergrund Nordhessen - This nice-looking, historically minded site exhibits industrial and military sites beneath North Hesse (in German).
Vimudeap - The Virtual Museum of Dead Places has fantastic clickable maps and photo galleries of underground sites around the world (in German).