When I read this post https://blogs.oracle.com/javamagazine/the-top-25-greatest-java-apps-ever-written?source=:so:tw:or:awr:jav::&SC=:so:tw:or:awr:jav::&pcode=What about very free java applications, frameworks, papers related with Java?
MuJava, WebSphinx, WEKA, Wiggle, Selenium, Alice (java learning for kids)
They are just only came to my mind in seconds :). I wanted to post this before I forgot.
;)