To output Japanese as something other than question marks in the Vista Command Window I have to wrap System.out like this:
PrintStream out = new PrintStream(System.out, true, "Shift-JIS");
Then I output to that instead. Shift-JIS is the code page Windows uses for the Command Window on my machine. I do have a lot of Windows settings flipped to Japanese, though. No clue about Linux.
You can change the default encoding for files in Eclipse here:
Window -> Preferences... -> General -> Workspace -> Text file encoding
You can change the encoding for a particular file by:
right-click on file in package explorer -> Properties -> Resource -> Text file encoding
Sometimes you have to close the editor and restart after that before it will let you save Japanese.
Eclipse seems to compile properly based on those settings without any special arguments. It has its own compiler anyway and doesn't use Sun's.
I haven't found a good way to set the default console encoding in Eclipse. Generally I run the file once then go to:
Run -> Open Run Dialog... -> Common tab -> console encoding
There is no Shift-JIS option there, but you can use UTF-8 or similar and then wrap like this:
PrintStream out = new PrintStream(System.out, true, "UTF-8");