When it rains in Japan there are two things to do: Food & Shopping!
Heck, you could spend a whole day in one electronics or fashion department store alone! Large stores are not just for shallow shopping, for example, Tokyu Hands gives you an amazing look into Japanese culture and is great fun.
Check out my blog (
Smart & Cheap Japan Travel) for some more ideas on those.
Anyway, as everyone said it's not that bad. Have fun!