Adapted from a SuperUser answer:

/etc/launchd.conf does not exist by default, but it does still work in 10.9.

1. Run for example sudo nano /etc/launchd.conf.
2. Add a line like 

   setenv M2_HOME /opt/boxen/homebrew/Cellar/atlassian-plugin-sdk/5.0.0/libexec/apache-maven-3.2.1/

3. Run 

   launchctl < /etc/launchd.conf
   
   sudo launchctl < /etc/launchd.conf

    and relaunch processes.