Duplicate Line Finder
To test case, you can use toLowerCase() and toUpperCase() methods in String to get case. Also using String, you can use the split(' ') method to get each word and compare them instead of using two lists. It would definately increase performance to some extent. 

To get the contents a bit better, the new nio package was updated in java 8 and has methods like Files.readAllLines(Path p);, returning a List (a list of lines) instead of using the BufferedReader trick. You can also use readAllBytes(Path p); which will return a byte array, but it is much easier to use readAlLines for your case.

Other than that I don't think there is much to give you. You have done a good job.