Is it possible to create a custom theme function? I want for example to create a mytheme_table function to override theme_table etc. (in template.php) but I do not want to use it everywhere in my project.

I need to replace the table with a div or to remove some hardcoded wrappers.

$output .= theme('table_custom', array('header' =&gt; $header, 'rows' =&gt;
$rows, 'attributes' =&gt; array('id' =&gt; $table_id, 'class' =&gt;
array('field-multiple-table'))));
you don't have to use hooks in your theme functions.   you could create your own function called theme_table_custom()  and use that in your template files.

if for some reason you must use the hook, you could include the original drupal code in the function and include a check for a table id or something, which would then fire your custom code.