vsDiffMerge.exe

Some command line options seem to include:

Merging non TFS files

Compare file-left.txt to file-right.txt, both of which are desencdents of file-base.txt:

vsdiffmerge.exe  file-left.txt  file-right.txt  file-base.txt  file-result.txt   /m

Apparently, in order to run this command from the command line, an instance Visual Studio must already be running.