How to comment out code in a .tpl.php template
I actually prefer to use this way

&lt;?php if (FALSE): ?&gt;
&lt;div class="meta"&gt;
  &lt;?php if ($submitted): ?&gt;
    &lt;span class="submitted"&gt;&lt;?php print $submitted ?&gt;&lt;/span&gt;
  &lt;?php endif; ?&gt;

  &lt;?php if ($terms): ?&gt;
    &lt;span class="terms"&gt;&lt;?php print $terms ?&gt;&lt;/span&gt;
  &lt;?php endif;?&gt;
&lt;/div&gt;
&lt;?php endif; ?&gt;


This make it easier to put the block back in (change FALSE to TRUE), or attach a variable to the conditional.

EDIT:

To address your example, I would do it one of two ways

&lt;?php if (FALSE): ?&gt;
&lt;?php if ($logo): ?&gt;
  &lt;a href="&lt;?php print $front_page; ?&gt;" title="&lt;?php print t('Home'); ?&gt;" rel="home" id="logo"&gt;
  &lt;img src="&lt;?php print $logo; ?&gt;" alt="&lt;?php print t('Home'); ?&gt;" /&gt;
  &lt;/a&gt;
&lt;?php endif; ?&gt;
&lt;?php endif; ?&gt;


or

&lt;?php if (FALSE &amp;&amp; $logo): ?&gt;
  &lt;a href="&lt;?php print $front_page; ?&gt;" title="&lt;?php print t('Home'); ?&gt;" rel="home" id="logo"&gt;
  &lt;img src="&lt;?php print $logo; ?&gt;" alt="&lt;?php print t('Home'); ?&gt;" /&gt;
  &lt;/a&gt;
&lt;?php endif; ?&gt;


I would normally lean towards using the second in my daily work.