Whether it is a restaurant or clothings shop, you can expect neatly formed lines everywhere in Japan.
Somehow in Japan customers are very patient and willing to wait for what they want.
I've encountered lines in several different situations.
Just for the restaurant, normally I would not want to wait too long to get a seating place in a restaurant, I would look for a different place. But in Japan people don't mind the waiting.
To enter a clothing store, when I was in Japan I only saw it happening when they opened a new "western" store, like H&M. But once I was in, I wanted to get out because it was too crowded.
The longest line ever was the line for the new year sale in Laforet, Harajuku.
I would not what to think of what would happen with lines like these in my country, it would be mass hysteria. But in Japan, everyone stays polite and neatly in line. Only when entering the department store there was a little bit of running, but no pushing!