Another free option is jmeld: http://keeskuip.home.xs4all.nl/jmeld/
It's a java tool and could therefore be used on several platforms.
But (as Preet mentioned in his answer), free is not always the best option. The best diff/merge tool I ever came across is Araxis Merge. Standard edition is available for 99 EUR which is not that much.
They also provide a documentation for how to integrate Araxis with msysGit.
If you want to stick to a free tool, JMeld comes pretty close to Araxis.
