xdiffr is an open-source cross-platform graphical differencing application. It has intuitive auto aligning diff views.
Windows and Linux binaries can be found at http://adamk.org/xdiffr/
To build from source you need Qt4 or Qt5.
You are more than welcome to fork this project and make changes. I will try to merge back in any changes that will have broad appeal.
The license is GPL v2. Please share any source code changes with the community.