A lot has been written on how the iPhone performs in Japan, the world’s most advanced mobile nation, but the general consensus in this country now is that it sells very well (even though both Apple and provider SoftBank Mobile refuse to break down Japan-specific sales numbers). It’s rumored that the number of iPhones sold in Japan has passed 3 million.

There are reasons for this success (super-low pricing, aggressive marketing, Apple’s pre-iPhone brand popularity in Japan, clever product positioning by SoftBank, etc. etc.), but we’re talking about a country in which basically every cell phone is a smartphone, a country where you’d be hard-pressed to find a handset without a digital TV tuner or e-wallet function, for example.

It’s big in Korea, it’s probably big in China’s grey market, and the iPhone continues to be big in Japan. According to a report [JP] released by Tokyo-based research company Impress R&D, the iPhone has captured a whopping 46.1% of the domestic smartphone market.

Would it be foolish to begin this story with the words “poor Microsoft”? I mean, the company isn’t exactly hurting for money, and yet it looks like 2009 was the year that the Xbox 360 finally died in Japan. Not that the Xbox 360 ever really did well in Japan, but this year it looks like everything fell off a cliff.

Look at this chart. It shows the sales of the various game consoles this year. You’ll immediately notice that sales across all platforms are down this year, which makes sense: the people who wanted a Wii probably hve a Wii by now, etc. The best selling console was the Nintendo DS (no doubt helped by the release of Dragon Quest IX), followed by the Wii, PSP (?!), PS3, PS2 (?!), and, lastly, the Xbox 360.

That’s right: the nine-year-old PS2 has outsold the Xbox 360 in Japan in 2009.

I’m not sure how much Microsoft cares, or should care. There weren’t too many (any?) Japanese games released exclusively for the system this year, so it probably wasn’t expecting… well, not monster sales, but respectable sales.

And then when you figure in that the Xbox 360 is so obviously a system designed and executed with the North American market in mind, and that Japan has always been an afterthought for the system, then you see where I’m going with this.

According to survey of 2,300 Japanese retail stores, the iPhone was #1 in customer popularity, beating out all of those crazy, wonky phones they sell in Tokyo with names like the WonderFetus 100 Softbank X200-900 and the Brad Pitt Special Edition E900 from Sanyo with built-in TV tuner, can-opener, and fishing lures.

Smartphone sales are growing in Japan and customers like the 8 and 16GB 3G models and Apple has sold 1 million iPhones through Softbank, a major Japanese carrier.

The BlackBerry Bold came in third and the rest of the list were phones by HTC.