How do I remove the 'always on top' feature of the applet?

Under config.treemap add the following (if you already have a <controller> tag, add the contents to your existing tag):

<controller>

  <noTrigger event="mouse"
             type="enter"
             button="all"
             clickCount="all"
             modifiers="all" />

  <trigger event="mouse"
           type="enter"
           button="all"
           clickCount="all"
           modifiers="all"
           action="${config.action['setFocus']}" />

</controller>

The first event removes all the triggers mapped to the enter event, including the requestKeyboardFocus action, while the second re-maps the enter event back to the setFocus action (which is what allows the popups to appear).

Then add the following under config:

   <action name="setFocus"
           type="custom"
           class="com.labescape.treemap.action.SetFocusAction" />