That is not true! JDownloader is released under GNU GPLv3, although it
contain some closed-source parts[1] (see the 'License' section on it's
Wikipedia article), like the non-free unrar[2]. I searched more about this
topic over the internet but does not found any valuable information regarding
which parts are they nor how to remove them. Maybe I will try to contact the
developers.
Because the project comes from Spain like Trisquel, you may know more about
it and can give me more information because that is all I know!
Wikipedia article about JDownloader:
https://en.wikipedia.org/wiki/JDownloader
Source code can be obtained here:
http://jdownloader.com/articles/source-code.html
Proof, that JDownloader has GPLv3:
https://trisquel.info/files/jdownloader-license.png
[1] Violates the GPL?
[2] Can be found at '~/.jdownloader/tools/linux/unrar/unrar'. It is
automatically downloaded during the first start (from
'http://update4ex.jdownloader.org/branches/last09/tools/linux/unrar/unrar').