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:
- KDiff3
- DiffMerge
- P4Merge
- Meld
- Beyond Compare Pro.
(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.)