The best open source alternative to Araxis Merge is Meld, which is both free and Open Source. If that doesn't suit you, our users have ranked more than 25 alternatives to Araxis Merge and 12 is open source so hopefully you can find a suitable replacement. Other interesting open source alternatives to Araxis Merge are WinMerge (Free, Open Source), KDiff3 (Free, Open Source), Compare (Free, Open Source) and WinMerge 2011 (Free, Open Source).
WinMerge 2011 series is a fork of the original WinMerge application that compiles without ATL/MFC dependencies to enable zero-budget developers to build WinMerge from sources using Visual C++ Express editions.
Meld is a visual diff and merge tool targeted at developers. Meld helps you compare files, directories, and version controlled projects. It provides two- and three-way comparison of both files and directories, and has support for many popular version control systems.