flake8.xml

<?xml version="1.0" encoding="UTF-8"?>
<toolSet name="Code Checking">
  <tool name="Flake8" showInMainMenu="true" showInEditor="true" showInProject="true" showInSearchPopup="true" disabled="false" useConsole="true" showConsoleOnStdOut="false" showConsoleOnStdErr="false" synchronizeAfterRun="true">
    <exec>
      <option name="COMMAND" value="/usr/local/bin/flake8" />
      <option name="PARAMETERS" value="--max-complexity=10 --max-line-length=100 $FilePath$" />
      <option name="WORKING_DIRECTORY" value="$ProjectFileDir$" />
    </exec>
    <filter>
      <option name="NAME" value="Filter 1" />
      <option name="DESCRIPTION" />
      <option name="REGEXP" value="$FILE_PATH$\:$LINE$\:$COLUMN$\:.*" />
    </filter>
    <filter>
      <option name="NAME" value="Filter 2" />
      <option name="DESCRIPTION" />
      <option name="REGEXP" value="$FILE_PATH$\:$LINE$\:.*" />
    </filter>
  </tool>
</toolSet>

Mac OS X:

drop this in ~/Library/Preferences/PyCharm30/tools
flake8 path most likely: /usr/local/share/python/flake8