From our awesome lead artist:
MD5 is a very old format, and most Maya exporters for it are not compatible with versions of Maya post 2009, so we must use Maya 2008 or 2009 to export at the end of the process. If you have a Maya subscription, Autodesk will allow you to download maya 2009 for free.
Once you have maya 2009 install the md5 exporter here:
http://scripts.zbufferstudios.com/
Help for the plugin can be found here:
http://www.doom3world.org/phpbb2/viewtopic.php?t=19710
The md5 format requires some specific set up with regards to rigging etc, so have a look at the following links to read up on it:
http://wiki.splashdamage.com/index.php/MD5_Export_Process
http://www.modwiki.net/wiki/MD5_(file_format)
If you can not source Maya 2009 from somewhere you can alternatively:
Export from Maya 2011 as an FBX 2006 file, then use FBX converter 2009 (old version available for free from Autodesks site) to convert to a legacy collada format then bring this in to Blender to export as md5, but that is convoluted.