Why is my field not showing up in the template?
Your code is right. If field_secondary_links is in $content, it should be rendering it out. You might want to double check that the field is named correctly. If you have devel installed, try using dpm($content) to make sure the field is in there, that it is named right, and the the correct data is getting pulled in.

EDIT =======================================================
If $content is unavalible for whatever reason, you can still render this from $node, but it's a bit diffrent. Your code should look like this:

&lt;div id="secondary-links"&gt;&lt;?php  print render(field_view_field('node', $node, 'field_secondary_links', array('label'=&gt;'hidden'))); ?&gt;&lt;/div&gt;


You can remove the array('label'=&gt;'hidden') from field_view_field() if you want the label to show up.

That should prerender and then render the field for you. Not sure why your $content is missing though, but this should be a workable work-around.