There's no one single consistent style followed by all applications. They are (broadly) synonyms. In truth it doesn't really matter so long as the expected audience understands what you mean.
Options are selections the user may make to change the behavior of the software (after it's been installed), including some things that might not have been in the initial default configuration.
Settings are options that are preserved between sessions (what an application does after it's been installed).
Preferences are options with more then one relevant choice in each catagory.
Configurations are entire sets of options, settings, and preferences saved in a file and loaded by the program on startup.