Pure Grain Bakery
's pumpernickel is one of the best German-style breads in these parts. Though it's 100% rye, the bread is lighter and less sour than most of this style, and it has a wonderful nuttiness that's accentuated by toasting. I first came across it several years ago in a bread basket at a German restaurant, and was so impressed that I asked where they got it. Unfortunately, it turned out that the bakery is in Vacaville, and at the time they had no retail outlets in SF.
Now they do. Lehr's German Specialties (1581 Church) carries both Pure Grain pumpernickel and a variety of German goodies that go well on top of it, such as apfelkraut (dark, not very sweet apple butter) and quark (soft German cream cheese), a classic breakfast combo, and various sorts of liverwurst. You can also get the bread at Rainbow Grocery