Go into phpmyadmin and drop the databases for the companies you no longer want.
Then go into config.php and delete the lines for the companies you no longer want that look like this under the
//Installed companies
heading
Code:
$CompanyList[0] = array('database'=>'weberpdemo' ,'company'=>'WebERP Demo Company' );
$CompanyList[1] = array('database'=>'sometest' ,'company'=>'Some Test company' );
$CompanyList[2] = array('database'=>'test2' ,'company'=>'Another Test' );
Of course leave the company you still need!