I have come back from Japan and I hope it may be useful for other people to add some notes about what I have done in Japan concerning mobile connections.
In general, voice calls also with a local SIM accessible to foreigners (i.e. SoftBank or PuPuru) seemed to me not much cheaper (and considering the cost of opening an account perhaps even less cheaper) than an European SIM in roaming I decided that it was not worth the cost and hassle to buy one.
Phone booths are everywhere in Japan and I would stick to them when I would be without Internet connection and VOIP.
I do not regret this decision. Occasions that would force me to phone from a normal phone where very limited (but I made bazillions of VOIP calls, I was not an isolated person!) and their cost negligible at the end of the game.
Neither I needed to receive calls, though in many places (car rentals, hotels, etc.) they actually ask for your mobile phone in order to contact you if there are problems. But, hey, you are in Japan! There never was a problem, nobody phoned me!
Data access: I opted for the PuPuru service. I chose the E-mobile service (I think it is a service provided by another provider that PuPuRu makes accessible to people not knowing a word of Japanese). In one month I spent about 150$ (but in Euros it sounds better!).
E-Mobile Rental Service?PuPuru: Cell Phone Rentals Japan
You get an USB key with self-installing software and unlimited traffic. I had it sent to the landing airport and getting it, even with jet lag and with the initial "Lost in Translation" effect it was a 5 minute matter to understand where I should go in the airport and get the package. You will then return it simply by using a self addressed already stamped envelope they provide and posting it in any postbox right before leaving Japan (also from the airport, if you want to use it till the very last second). As simple as that.
The key worked immediately with my Netbook.
Comments: the service provides exactly what they say. You get about 1.5 Mbit/s inbound bandwidth and about 500 Kb/s outbound (Maximum is / Mb/s, but as everywhere you never reach this limit).
Coverage is by far not comparable to the 3G network. Though it uses (if I am not wrong) a 3G network (maybe a subset of the DoCoMo network) you may be in places with 3g coverage but no Internet access.
Coverage is good in cities, along main railways and highways. No go in mountains or hills (if steep, which is always the case in Japan!). Anyway you can check the coverage on their site and the maps are accurate. No cheating.
When the signal is present you can do practically everything. Handovers work, so you can begin a VOIP conversation in your car and it lasts while you are traveling until you are under coverage.
All in all, it works great.
The VOIP calls alone repaid themselves the cost of Internet access, let alone the use of Internet which is getting more and more useful when traveling, even in Japan where language barriers also in the Web are still huge (though things are rapidly getting better).
Cons: sometimes you would like the coverage would be wider. You might be in that wonderful corner of Japan, but without coverage and plenty of 3G signal around you.
You must use the USB dongle. It is not allowed to put the SIM in other devices. Therefore at least in principle you cannot use your smartphone to connect to Internet. This limits a bit your flexibility, being bound to use a PC which as small it can be, cannot be carried everywhere.
I sticked to the rules and I was not curious as I am always am. The service was too useful for me to look for problems in experimenting. I guess that introducing the SIM in a 3G phone and configuring the right APN (which is clearly given in the documentation) it would work. But for this time I was not willing to take chances. Maybe next time!
When I was out of E-PuPuRu coverage I used my BASE SIM on DoCoMo and with all the tricks to limit data exchange (be sure to block ALL autoupdating features of the Operating system, anitviruses, etc. There are always some that slip out of your control!) I could at least check and send emails without needing to sell my house.
Cheers,
Sleepy