Beyond Compare 3 is out in beta. It supports 3 way merges!
I found this out literally minutes before I started what turned into a 2 day mergeathon between two large and divergent branches in TFS, with *lots* of merge conflicts to manually resolve, and I can honestly say I'd probably still be merging if I hadn't downloaded it. It's just fantastic.
I'll probably post some screenshots etc... soon, but if you're struggling merging with BC2 and/or the built-in diff/merge support then you really should check it out.
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