I used this module to create an alternative to admin/content and it works great. I found I had to add one line of code to make it work, in ajaxtable.module ln 299:

 $search_values[] = $_GET[$id . $input['id']];

BTW, here is my form code, which is joining the node table to the user table:

function ajaxtable_table_nodesearch($override='') {
 $table = array(
   'edit' => true,
   'delete' => true
 );
 $search_inputs = array(
   array(
        'type' => 'text',
        'id' => 'author_search',
        'help_title' => 'Author Search',
        'help' => 'Search by UserName of Author',
        'operator' => 'like',
        //'jointable' => 'users',
        'col' => 'jt.name',
        'size' => 8
    )
 );
 $inputs = ajaxtable_search_inputs($search_inputs);
 $theme['search'] =  '
   <table class="ajaxtable-default-search-table">
    <tr>
     <td class="ajaxtable-default-search-table-left"></td>
     <td>{search_help}</td><td>Search for {search_input} </td>
     <td> | With this username: ' . $inputs['author_search']['input'] . '</td>
     <td>' . $inputs['author_search']['help'] . '</td>
     <td>{search_button}</td>
     <td class="ajaxtable-default-search-table-right"></td>
    </tr>
   </table>
   ';
 $override = array(
  'search_inputs' => $search_inputs,
  'theme_override' => $theme,
  'query' => ' SELECT * FROM {node} as n INNER JOIN {users} as jt '
            .' ON n.uid = jt.uid ',
  'columns' => array(
   array(
    'col' => 'nid',
    'label' => 'ID',
    'sortable' => TRUE,
    'searchable' => TRUE,
    'help' => 'The unique node ID.',
   ),
   array(
    'col' => 'title',
    'label' => 'Title',
    'sortable' => TRUE,
    'searchable' => TRUE,
    'help' => 'The title of the node.',
   ),
   array(
    'col' => 'name',
    'label' => 'AuthorName',
    'sortable' => TRUE,
    'searchable' => TRUE,
  //  'callback' => 'ajaxtable_col_authorname',
    'help' => 'Nodes authored by this authorname',
   ),
  ),
 );
  ajaxtable_override($table,$override);
  return $table;
}