I saw this posting which explained how to get BC3 working as the diff tool for Subversion... but what about using Beyond Compare 3 to do 3-way merge/compares?
I like liamf's batch file, but I think it could take a minor tweak:
I've added automerge and reviewconflicts to the command invocation, so that in case of a merge without conflicts it just closes without intervention - the UI will only pop-up to review conflicts.
Thus, the line in question becomes:
%DIFF3% /automerge /reviewconflicts /lefttitle=%MYTITLE% /centertitle=%OLDTITLE% /righttitle=%YOURTITLE% /outputtitle="Merge Output" %MINE% %YOURS% %OLDER% %OUTPUTFILE%