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Our hosting comes with "Horde" web mail client that does offer a Japanese language interface, but this does not display correctly on the screen no matter what encoding I select. The email contents have the same problem.
The only solution I have thought of is Hotmail with optional extra of accessing pop accounts.
There must be other free web mail services or web mail clients that would work with pop account in Japanese.
Have you tried the standard Japanese Hotmail or Yahoo Mail accounts? They can certainly handle the encoding on the sending and receiving end. A lot of the big portals used to have free e-mail accounts, but I'm not sure whether any of them can handle POP accounts.
Although it's in beta now, I've been testing out GMail, and it seems to have no problem with Japanese or Chinese e-mail. They don't have a POP account yet, but I have just been forwarding a few of my accounts through, and it works quite well for a web based account. I really like the interface and ease of use...I don't want to sound like a GMail shill, but it is the only webmail app I consider usable.