My wife made fun of me when I bought The Little Tokyo Subway Guidebook: Everything You Need to Know to Get Around the City and Beyond. It turned out to be the best guide to the Tokyo subways I found.
What makes it invaluable is the book abandons maps that bear any relationship to geography. Instead, each subway line is mapped out in a simple straight line - all the stops top to bottom. You can track down which exits to use to get to specific places, where to connect to different lines, and even plan out travel times.
My only regret is there isn't an updated edition. I'll keep dreaming of that.