I have to rofl, as I shot much good video in arcades and was smoking at the time, I had a staff member approach me (I thought to tell me to stop filming) and offer me an ashtray to stub out my smoke.
YouTube - Japanese Arcade games megamix

Japanese clothing stores generally don't allow you to take pictures and I know that quite a few smaller boutiques (or places like the 109 building, I've heard) will approach you and tell you to stop or leave.

I'm going to agree with the take photos first, apologise later approach. I took photos everywhere I went (aside from the inner parts of temples, where I thought it would be best to be respectful) with my chunky DSLR, and the only place I was told to stop was in a pachinko parlour. Even then, I was told off in an extremely apologetic way with much bowing - you're not going to get arrested or thrown out or anything.

Japanese packaging is fantastic, if kind of over-the-top and non evironmentally friendly XD I bought some packets of lollies and things just for the packaging sometimes.

Thanks for all the tips, everyone!
 

Hearing about your experiences makes me that much more excited for my trip next month. I've been practicing taking sneaky photos at my local Mitsuwa Market here in L.A. and the pictures are coming out great without flash! God bless Sony's little compact cameras.

Well, pachinko parlors are definitely on my "hit list" as well, so hopefully I will have mastered spy photography by the time I visit one. I mean, how can I NOT take a pic of a pachinko machine in Tokyo? Here in Southern California in the 1970s (dating myself here), every suburban family room had an old, refurbished pachinko machine in it. You know, the really old-school kind where you had to flip the lever for each shot.

Thanks again for all your helpful info!

I've never had any issues in Japan and people seem overly happy to receive and have photos taken. I think Japan is the land of the camera!

I guess what you may need is da Japanese translation of "Excuse me, would you mind if I take a photo" "Are photos allowed", etc.

I'm sure some will post the wording in English characters for you:vsign:

I did manage to sneak a couple in the pachinko parlour before they got me, so I'm sure you'll be fine with a compact camera ^_~ Good luck!

Oh, someone with better Japanese might want to check this, but "Is it okay for me to take a photo?" is:

Shasshin o tottemo ii desuka
(or more phonetically: shya shin o tot temoe ee dess kah)

And get ready to hear "sumimasen ga..." (I'm sorry, but...)