Beyond Compare and Winmerge are tools that can be used to compare files in Windows, but the latter is not available in Linux and the former is only available as a commercial application. One alternative is to use Meld, a diff and merge tool for Linux. This open source program is a GUI for diff2 and diff3 written using pygkt toolit based on Python, Glade and GTK+.
This is not as powerful as the two programs aforementioned, but still very useful. It can also compare 3 files at the same time.
To install it in ubuntu:
sudo apt-get install meld
It will still allow you to compare files, directory and merge changes. The file comparison merge function is a little confusing at first, but after a while you’ll get used to it. Meld can also support version control comparison with CVS, SVN, GIT, Bazaar-ng or Mercurial.