- When cycling on the road always cycle on the left, don't argue just do it.
- Obey the rules of the road as if you were driving a vehicle.
- Don't run red lights but expect cars to rush through the intersection on orange and fresh red lights, especially taxis.
- Don't get doored. Ride a safe distance from parked cars taking the lane if necessary. Beware of delivery vehicles whose drivers tend to exit their vehicles in a hurry without looking.
- Beware of taxi's as they tend to pull into and out of traffic giving little or no warning. Also look out for automatically opening taxi doors.
- Wet manhole covers and freshly painted road markings are slippery, as are rail lines.
- Don't jump from the road to the sidewalk and back without looking. Choose where you're comfortable riding and stick with that choice. If you choose to ride on the sidewalks ride slowly and respect pedestrians.
- If parking your bicycle on the sidewalk do not let it block pedestrians.
- Register your bicycle, its compulsory but there are no penalties for not doing so. Being registered will help you avoid awkward situations with the police and it helps you prove ownership if your bicycle is stolen or impounded.
- Lock your bicycle no matter its worth. Japanese bicycle thieves are opportunistic and go for easy, unlocked, targets.
Despite widespread ignorance and poor enforcement of cycling laws in Japan cycling here just works. It works largely due to a set of unspoken yet socially observed rules, many of which don't reflect the law, but which have been crafted by society over the years.
The best way to learn how to cycle in Tokyo is to observe the cyclists around you, you'll soon learn what is socially acceptable. But I advise you pass your own common sense filter over your observations because there are many practices in which Japanese cyclists engage that they deem acceptable, but will challenge your own view on personal safety.