Shoes
Shoes come off when entering a home, many ryokan, some traditional restaurants, and any space with tatami flooring — look for a step up and a shelf or shoe lockers at the entrance as the signal. Slip-on footwear makes this a lot less friction throughout a trip.
On the trains
Phone calls are generally avoided on trains, and carriages tend to be noticeably quiet even when full. Priority seating near carriage ends is reserved for elderly, pregnant or disabled passengers even when it looks empty.
Chopsticks and eating
Avoid sticking chopsticks upright in a bowl of rice, and don't pass food directly from one set of chopsticks to another — both gesture visually toward funeral rites and are considered bad form at a meal. Eating while walking down an ordinary street is generally frowned upon outside food-stall areas built for it, like inside Kuromon Ichiba Market.
Rubbish bins are scarce
Public rubbish bins are far less common in Japan than in most countries, largely a legacy of past security concerns. Carrying a small bag for your own rubbish until you pass a convenience store or train station is standard practice for both locals and visitors.
The Osaka escalator exception
Almost everywhere else in Japan, people stand on the left side of an escalator and leave the right side clear for walking. Osaka famously does the opposite — stand on the right, walk on the left — one of the city's small, genuine local quirks, and a minor giveaway if you've just arrived from Tokyo.