Different citations carry different numbers of points, but overall Japan's point system is strict: Just a few minor traffic violations will have your license suspended, and frequent repetition will quickly get your license revoked. Let's take a look at the actual numbers:
The handy Compendium of Driver's License Questions website has put together the following chart, slightly tweaked into English by us.
So, what does all this mean?
Suspension (免停＝免許停止, mentei)
When your license is suspended, you retain possession of it, but you are not allowed to drive on it for the specified period of time (indicated in number of days at the top of the chart: 30日, 60日, etc.) Driving during this period is classified as driving without a license, which offence carries enough points to ensure that your driving privileges will be revoked. Traffic safety courses (免許停止処分者講習, menkyo teishi shobunsha koushuu) are available to take to reduce the number of days on a suspension, but the courses are usually only available during business hours on weekdays.
Revocation (免許取消, menkyo torikeshi)
When your license is revoked, it is taken from you entirely. The time periods indicated in the chart above (1年, 2年, etc.) are called 欠格期間, kekkaku kikan, are represent the amount of time before you will be allowed to apply for a new license. In other words, if your license is revoked, it will not be returned to you, ever. You will have to start from scratch at a driving school--or more likely the test center at a licensing center, as many driving schools will refuse to enroll individuals who have lost their licenses--and obtain a new driver's license if you wish to continue driving. By the way, in Japan, driving while intoxicated is an offence that carries enough points for immediate revocation.
Past Offences (前歴, zenreki, lit. "previous history")
As you can see in the chart, fewer points result in harsher penalties if you have accumulated a number of past offences. Your number of past offences is based on the number of times your license has been suspended. This number continues to accumulate until you pass one consecutive calendar year without being cited for any traffic violations, after which it is reset to zero.
Standing Number of Points (違反累積点数, ihan ruiseki tensuu)
Handled similarly to past offences, the standing number of points on your license continues to accumulate until it is either suspended (points return to 0 at the end of the suspension period), revoked (you lose your license), or you pass one full calendar year without any traffic violations (points return to 0).
Events such as your license expiring and being reissued or your birthday passing are irrelevant to this timeframe. The only concern is the date of your last citation--or, more correctly, the date at which you received official notification (usually by postcard) of your violation and paid the applicable fines or other punishment.
Safe Driving Incentive
On the other hand, if you go for two full years without any violations, there's a perk: Points for subsequent violations will not accumulate for a full year but only for the next three months, after which your total number of points will return to zero. If you have two violations within three months, or if your license is suspended, however, you lose this status.
Furthermore, if you pass five consecutive years without any traffic violations and without any accidents*, your license will be reissued in a fancy gold color to indicate that you are an outstanding(ly safe) driver. This will in turn ease your license renewal process and reduce your insurance premiums.
*Reported accidents, that is. That late-night scuff against a telephone pole or nudge against a parked car in a dark alley don't have to count.
Lesson in point? Avoid citations. They'll get you mired up quick.