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 only have experience with BC3 and TFS, so take this with a grain of salt. The 3-way merge was the only feature I had problems with. More than once I had to copy and paste the changes by hand in BC3 to finish the merge.