How to configure kdiff3 instead of emerge as a git mergetool?

Recent Git versions have built-in support for kdiff3, so there's no need to configure it manually using the generic cmd and args settings. Instead do:

$ git config --global merge.tool kdiff3

And if kdiff3 is not in your PATH environment also do:

$ git config --global mergetool.kdiff3.path /Applications/kdiff3.app/Contents/MacOS/kdiff3

This makes git mergetool launch kdiff3. Note that there is no way to configure Git to automatically launch your merge tool after a manual merge that has conflicts.

In case you really want to see how Git is calling kdiff3 internally, take a look at the built-in mergetool configuration for kdiff3.

Edit: For Beyond Compare 4, which now also supports Mac OS X, simply exchange kdiff3 with bc3 (yes, "3") and adjust the path in the above lines. Starting with Git 2.2.0 you'll be able to use bc as an alias for bc3 so that you do not have to care about the version number.

Recent Git versions have built-in support for kdiff3

Yes, but only Git 2.12 (Q1 2017) will allow those built-in tools to trust their exit code.

See commit 2967284, commit 7c10605 (29 Nov 2016) by David Aguilar (davvid).
^{(Merged by Junio C Hamano -- gitster -- in commit c4a44e2, 16 Dec 2016)}

mergetool: honor mergetool.$tool.trustExitCode for built-in tools

Built-in merge tools contain a hard-coded assumption about whether or not a tool's exit code can be trusted to determine the success or failure of a merge.
Tools whose exit codes are not trusted contain calls to check_unchanged() in their merge_cmd() functions.

A problem with this is that the trustExitCode configuration is not honored for built-in tools.

Teach built-in tools to honor the trustExitCode configuration.

(See kdiff3)

Extend run_merge_cmd() so that it is responsible for calling check_unchanged() when a tool's exit code cannot be trusted.
Remove check_unchanged() calls from scriptlets since they are no longer responsible for calling it.