If you need to modify data in the node body during the migration process, you can use prepareRow($row).

The following example displays how to call the user defined method "convertWiki2Html" which converts the node body from wiki markup to HTML:

  // manipulate the source rows
  public function prepareRow($current_row) {   
    $current_row->body = $this->convertWiki2Html($current_row->body_text,$current_row->page_title);  
  } 

  public function convertWiki2Html(&$body,&$title){
    // convert $body from mediawiki to HTML here...
  }

You can also add one or more callbacks when adding field mappings, like in this example from wine.inc (part of the migrate_example module) that adds two callbacks to the body field:

    // TIP: You can apply one or more functions to a source value using
    // ->callbacks(). The function must take a single argument and return a
    // value which is a transformation of the argument. As this example shows,
    // you can have multiple callbacks, and they can either be straight
    // functions or class methods. In this case, our custom method prepends
    // 'review: ' to the body, and then we call a standard Drupal function to
    // uppercase the whole body.
    $this->addFieldMapping('body', 'body')
         ->callbacks(array($this, 'addTitlePrefix'), 'drupal_strtoupper');