I found myself needing to change the end of line character in NetBeans. This was easily done by adding -J-Dline.separator=LF as a parameter to application launch path.
When using NetBeans under Windows, this is how the shortcut target looks like:
"C:\Program Files\NetBeans 7.0\bin\netbeans.exe" -J-Dline.separator=LFOther options are CR or CRLF.