Take a walk through a light industrial area. That's where the true Japanese font wonders lie. You'll find bizarre interpretations our our alphabet, grungy kanji stencil fonts and clunky scripts with descenders chopped off. Bonus: slogans such as "We love wood and humans!"

Bonus: slogans such as “We love wood and humans!”
Be sure to visit a couple of 100 yen stores for those, too:

Apart from that, just walking around can already be total typographic input overload. I second the restaurants – lettershapes everywhere, some beautiful calligraphy (and/or funky stuff). But even just stenciled signs, traffic directions painted on streets, or LED signs are just… amazing. I found it especially funky how the different alphabets/scripts are combined and interchanged (like here).

BTW if you're in/near Tokyo, and interested in graffiti: while Tokyo doesn't seem to have any really, Yokohama does.