Each of these hooks appears to exist [see notes on where it is invoked with
module_invoke_*() or module_implements() loop or drupal_alter()], but is not
documented that I could find.

hook_ajax_render_alter  [see function ajax_render() in includes/ajax.inc]
hook_archiver_info_alter [see function archiver_get_info() in includes/common.inc]
hook_batch_alter [see function batch_process() in includes/form.inc]
hook_countries_alter [see function country_get_list() in includes/locale.inc]
hook_cron_queue_info_alter [see function drupal_cron_run() in includes/common.inc]
hook_date_format_types_alter [see function _system_date_format_types_build() in modules/system/system.module]
hook_field_attach_purge [see function field_purge_data() in modules/field/field.crud.inc]
hook_field_extra_fields_alter [see function field_extra_fields() in modules/field/field.module]
hook_field_languages [see function field_multilingual_available_languages() in modules/field/field.multilingual.inc]
hook_field_purge_field [see function field_purge_field() in modules/field/field.crud.inc]
hook_field_purge_instance [see function field_purge_instance() in modules/field/field.crud.inc]
hook_field_storage_purge [see function field_purge_data() in modules/field/field.crud.inc]
hook_field_storage_purge_field  [see function field_purge_field() in modules/field/field.crud.inc]
hook_field_storage_purge_instance  [see function field_purge_instance() in modules/field/field.crud.inc]
hook_field_storage_update_field [see function field_update_field() in modules/field/field.crud.inc]
hook_field_ui_view_modes_tabs [see function field_ui_view_modes_tabs() in modules/field_ui/field_ui.module]
hook_field_update_forbid [see function field_update_field() in modules/field/field.crud.inc] --- NOTE: Seems to be documented as field_update_field_forbid in field.api.php? I think it may have been renamed? Also field_sql_storage_field_update_forbid() in field_sql_storage.module's doc header still refers to the old name?
hook_filetransfer_backends [see system_get_filetransfer_settings_form() in modules/system/system.module]
hook_language_init [see drupal_language_initialize() in includes/bootstrap.inc]
hook_language_switch_links_alter - filed a separate issue on this one http://drupal.org/node/675144 because there were other problems
hook_rdf_namespaces [see drupal_get_rdf_namespaces() in includes/common.inc]
hook_search_page [see search_data() in modules/search/search.module]
hook_themes_disabled [ see function theme_disable() in includes/themes.inc]
hook_themes_enabled [ see function theme_enable() in includes/themes.inc]
hook_token_info_alter - See issue http://drupal.org/node/673462
hook_trigger_info_alter [see function _trigger_get_all_info() in modules/trigger/trigger.module]
hook_updater_info [see function drupal_get_updaters() in includes/common.inc]
hook_updater_info_alter [see function drupal_get_updaters() in includes/common.inc]
hook_verify_update_archive [see function update_manager_archive_verify() in update.manager.inc]