Java
docomo
Almost all docomo handsets support Java, in the form of either DoJa or Star profile (Star profile is backwards compatible with DoJa)
au
au first introduced Java support with EZ Appli, however the last phone to support it was released in 2004 and supported a maximum JAR size of 150 KB. From summer of 2007, KDDI has introduced support for Java again through Open Appli, with a maximum JAR size of 300 KB.
SoftBank
Most SoftBank handsets support Java (MIDP profile).
Unlike applications for Docomo and KDDI, SoftBank applications cannot be downloaded from anywhere on the web. Instead it must be downloaded through a trusted domain. There appears to be only one company acting as a trusted domain to businesses, which charges between ¥78,750 and ¥245,700 per three months of making the application available to the public.
Resources
Mobile Developer Lab - Discussion about Japanese mobile phones oriented around Java (specifically DoJa)