presave like option for adding vocabulary and terms similar to one provided by hook_nodeapi
You can add a validation function to the form in hook_form_alter(). If you give your module a high weight, that validation function will be added last to the validation functions array and thus be executed last. The validation function can call form_get_errors to check whether errors occurred. If no errors occurred, you can be pretty sure that the vocabulary or term will be saved to the database, making it something like hook_nodeapi($op = presave').

Note that you cannot use hook_form_FORM_ID_alter(), because these hooks are executed before hook_form_alter(). Also, I found no easy way to react on the installation of other modules.