FileMerger and other “Diff-Tools” normally compare only two files at once. Good programs (like BBEdit) can additionally compare the contents of two folders.
Today I had to compare 673 files in two folders with each other. Now I was looking for a tool doing this for me: I found KDiff3!
KDiff3 can not only compare a huge amount of files in two different locations, it also compares three files with each other at once. KDiff3 is easy to use and has a functional GUI, which looks like a Win 3.11 GUI
You can download that tool for Mac Universal (PPC/x86), Linux i386 and Windows i386 from its homepage at: http://kdiff3.sourceforge.net/