Dynamic hook registration
The usual approach is to create a settings form for your module and save the content types on which you want your hook_form_alter to intervene. Then with a simple check you can implement you alterations.
The list of content types existing at a certain point in Drupal is easy to check.

I see no other way of actually placing your alters for specific content types. Even if you create your hook dynamically by using an unorthodox 

foreach ($SELECTED_NODETYPES as $NODETYPE) {
  if (!function_exists("my_module_form_$NODETYPE_node_form_alter")) {
    function my_module_form_$NODETYPE_node_form_alter (&amp;$form, &amp;$form_state) {
        //your alterations
    }
  }
} 


You will still have to have a list of nodetypes to check from, and on each new nodetype creation you have to be sure you flush the cache so your module will declare the new hooks and Drupal actually will take them into account.