Beyond Compare 3 Pro supports three-way merging, and it is a pretty impressive merge tool. It's commercial (but worth it, IMHO) and is available on Windows, Linux, and Mac OS X.
As pointed out in a comment, it's also inexpensive.
Note: If one does not have a merge set, that is, merge markers resident in the destination file, Beyond Compare does not offer three-way file compare/editing. Beyond Compare says that feature is on their list.
Note: 3-way merge is a feature in the Pro edition of Beyond Compare 3 only