Note: this list is generated by looking for the string for this theme hook, so it may include some references that are not actually using this theme hook.

file_file_formatter_file_image_settings in core/modules/file/file.module
Implements hook_file_formatter_FORMATTER_settings().
file_settings_form in core/modules/file/file.admin.inc
Form callback for file settings.
system_theme in core/modules/system/system.module
Implements hook_theme().
system_token_output in core/modules/system/system.pages.inc
Page callback to output a token tree as an empty page.
theme_token_tree_link in core/modules/system/system.theme.inc
Theme a link to a token tree either as a regular link or a dialog.
token_example_example_form in modules/examples/token_example/token_example.module
Form builder; display lists of supported token entities and text to tokenize.