I just checked out the watchdog section, and there are a few code and code style things I'd like to point out.
All template.php files must begin with:
<?php
// $Id$All .tpl.php files must begin with:
<?php // $Id$ ?>All function overrides in template.php should begin with a comment that at the very least provides a URL
to the api.drupal.org documentation for that function:
/**
* Documentation:
* http://api.drupal.org/api/5/function/theme_watchdog_form_overview
*
*/If significant changes were made to the function in order to separate the content and the layout, this
may be documented. Likewise, this may also document obvious alternatives. Further documentation
is optional.
The use of form_render in the .tpl.php file doesn't work due to references. Therefore, all form renders should look like this:
<?php
$vars = array(
'form' => drupal_render($form),
);
?>And then passed into the _phptemplate_callback function.
It is preferable to indent the contents of a div in a .tpl.php file like this:
<?php // $Id: watchdog_form_overview.tpl.php,v 1.5 2007/02/04 22:42:27 merlinofchaos Exp $ ?>
<div class="container-inline">
<?php print $form; ?>
</div>This makes it more clear; sure it wastes a little whitespace but this is going to happen at the presentation layer.
Try to keep consistent indentation levels where possible.
In .tpl.php files, it is best to prefer if...endif to if {}. Example:
<?php if ($condition): ?>
<span>foo</span>
<?php endif; ?>I find that this structure is easier to read when mingled with HTML, and I think designers will too.
I'm sure more items will be added to this post later.

Comments
BAH! <code> doesn't preserve
BAH! <code> doesn't preserve indent level. It does on drupal.org -- I wonder what happened there.
Using a combination of
Using a combination of <code> and <pre> will.
Just to be 100% clear, is
Just to be 100% clear, is this what you mean?
or