To the absolute majority of users, they're all the same. Users aren't going to go "Ok, I'm looking for Preferences, and this here thing says Settings, so it must not be what I need".
Most of the problems with unclear terms arise from exactly this type of backstage dilemmas - the techie developers say that Preferences isn't exactly the right term, because in our app it's actually closer to Settings - while the difference between the two is only clear to the devs (and their mind is not totally made up either). There recently was either a blog post or a question here that discussed Clarity vs. Accuracy, but I can't find it right now. The bottom line is that for the users, Clarity comes first. That is to say that the actual semantic differences between these terms are too subtle to take them into account. Treat them as complete synonyms, unless you need to use more than one term in the same app.
As to which one to use after all - there's a number of factors that may help you decide. Platform standards, similar apps, appropriate icons, space available ("configuration" is much longer than "options"), terms used elsewhere in the app (if you're already using one of those terms in a different setting, you might want to either differentiate between the two, or tell the user that they're similar). Sometimes it can be something as "superficial" as looking at other items in the same navigation level and selecting a term which has a non-recurring initial letter, to make it easier to recognize it in the list.