I've had an iPhone 2G from day one, and I've somewhat well researched the 3G and its Japanese capabilities.
First of all, if you already have an iPhone 2G or iPod Touch, software wise you'll be fine-- all three devices will run the exact same firmware, although iTouch users will have to pay a nominal fee for it. Otherwise, the main advantages of buying an iPhone 3G are better battery life(?), GPS, and 3G. Software-wise, they're all the same.
Next, as far as Japanese input goes, the iTouch has had input from almost the beginning, and the iPhone has had it since 1.1.1, although some hacking was required. In firmware 1.1.1, the Japanese input was actually present, although you had to change a preference file to make it appear in the options. Since 1.1.2, however, those support files were removed -- although some enterprising developers copied the support files from the iPod Touch, and made a hack to install them via Installer.app if you jailbreak your iPhone.
As of 2.0, Japanese input will be available on all devices, no hacking required. A Japanese version of the QWERTY keyboard will be available (type in romaji, predicts how to change it into kanji/katakana/hiragana/etc) as well as Japanese keitai style input (press the 2 key to switch between あ>い>う>え>お and such).
As I mentioned on another thread, the kanji drawing is actually part of the Chinese input method, NOT the Japanese. It apparently supports both Simplified and Traditional Chinese, but how close either or both are to Japanese kanji I don't know -- I know very little about Chinese. So, in other words, if Japanese kanji are similar to Traditional or Simplified Chinese kanji, then that input method will be very useful -- if not, then... not so much.
In terms of actual apps, wedict works fine for me, although it only has EDICT... so it's good in a pinch, but it's more of an emergency dictionary than anything.
The makers of iFlash and Mental Case, two flashcard apps for the Mac, have already stated that they're working on iPhone versions of their software. Seeing as how I use Mental Case, I'm pretty excited about that. Unfortunately, if you're not using Mac OS and want desktop<->iPhone/iTouch flashcard fun, I'm not sure what your options will be with those two apps.
Other random notes:
* Even in the US, if both iPhones support Japanese input, I can send and receive SMSes in Japanese with no trouble.
* You *can* send email to Japanese keitais, but since the iPhone uses Unicode, not all Japanese keitais will be able to read your mail; having said that, I have yet to receive something *I* couldn't read. In my experience, anyone with a relatively new DoCoMo keitai can read my mails no problem. My big question is when the iPhone launches in Japan, what they're going to do about this -- obviously they're not going to get everyone to switch from keitai mail to SMS over there. If they understand anything about the Japanese keitai use, they'll fix this and theoretically the fix would be universal.
* Mixi and other Japanese websites work great out of the box -- no hacking required, meaning anki's internet site ought to work, but I haven't tried.