I suspect the issue is not with NetBeans, but rather with whatever
program (probably some sort of shell, like cmd or bash, or perhaps
NetBean's integrated console) is interpreting the data sent via standard
out.

   I'm surprised you know enough to know the "original" meaning of \r,
and yet never experienced the behaviour of treating \n and \r as both a
carriage return followed by a newline until now. Have you been
cryogenically frozen or something?

   - Oliver

The problem is not, what gets written out to System.out,
but rather how much effort netbeans does to emulate a
real terminal. Obviously this effort does not go far
enough to distinguish between \r and \n.

I just tried with netbeans 5.5: same result.
Then I run the same .jar file from a real
terminal, and I see the expected "javaome".

If you replace the \r with a few \b's, you'll see
that netbeans doesn't even handle backspaces as
such, but instead writes them as white rectangles.