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Subversion, Git, Mercurial and others support three-way merges (combining mine, theirs, and the "base" revision) and support graphical tools to resolve conflicts.
What tool do you use? Windows, Mac OS X, Linux, free or commercial, you name it.
Here's a few that I've used or heard of, just to get the conversation started:
(I recognize that this is sort of like the Best Diff Tool, but it's different in that I explicitly focus on three-way merge tools; WinMerge is off the list, for example.)
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Perforce, the company best known for its enterprise version control platform, also offers a solid diff tool: P4Merge is free of charge and comes with a basic feature set that makes it an interesting option on Windows, macOS and Linux.
3-way merges use a dedicated commit to tie together the two histories. The nomenclature comes from the fact that Git uses three commits to generate the merge commit: the two branch tips and their common ancestor.
DESCRIPTION. Use git mergetool to run one of several merge utilities to resolve merge conflicts. It is typically run after git merge. If one or more <file> parameters are given, the merge tool program will be run to resolve differences on each file (skipping those without conflicts).
KDiff3 open source, cross platform
Same interface for Linux and Windows, very smart algorithm for solving conflicts, regular expressions for automatically solving conflicts, integrate with ClearCase, SVN, Git, MS Visual Studio, editable merged file, compare directories
Its keyboard-navigation is great: ctrl-arrows to navigate the diffs, ctrl-1, 2, 3 to do the merging.
Also, see https://stackoverflow.com/a/2434482/42473
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