After moving from the 2.x branch to 3.x i noticied that nodecomment_notify submodule was stripped out - fortunately the old code seems to work just fine with 3.x. For the purposes of supporting an older site I've copied nodecomment_notify into its own module: https://github.com/bnchdrff/nodecomment_notify

If there is interest we could add this module as a drupal.org project.