You can make "select all/unselect all" disappear by including the following line inside your table class:
$this->xsl_params['noselect'] = 'y';
You can make "show 10/show 25/show 50/show 100" disappear by including the following line inside your table class:
$this->xsl_params['noshow'] = 'y';
You can make the action bar disappear by removing all the entries in the global variable as follows:
$GLOBALS['act_buttons'] = array();
The navigation bar only appears if the current task has entries on the nav_button table. If buttons have been defined they will appear.
Messages only appear if the current script has generated any messages. If you don't want the message line to appear then don't generate any messages.
You cannot selectively turn off the help line or the pagination area.