I actually prefer to use this way
<?php if (FALSE): ?>
<div class="meta">
<?php if ($submitted): ?>
<span class="submitted"><?php print $submitted ?></span>
<?php endif; ?>
<?php if ($terms): ?>
<span class="terms"><?php print $terms ?></span>
<?php endif;?>
</div>
<?php endif; ?>
This make it easier to put the block back in (change FALSE to TRUE), or attach a variable to the conditional.
EDIT:
To address your example, I would do it one of two ways
<?php if (FALSE): ?>
<?php if ($logo): ?>
<a href="<?php print $front_page; ?>" title="<?php print t('Home'); ?>" rel="home" id="logo">
<img src="<?php print $logo; ?>" alt="<?php print t('Home'); ?>" />
</a>
<?php endif; ?>
<?php endif; ?>
or
<?php if (FALSE && $logo): ?>
<a href="<?php print $front_page; ?>" title="<?php print t('Home'); ?>" rel="home" id="logo">
<img src="<?php print $logo; ?>" alt="<?php print t('Home'); ?>" />
</a>
<?php endif; ?>
I would normally lean towards using the second in my daily work.