Still in rough development, a new extension for Google Chrome puts in your hands a useful power tool for separating your data from Facebook apps of dubious origin. Called OOptOut (download), the add-on by Chad Selph helpfully lists above the Facebook header for you any permissions that a newly-installed Facebook app requests.
Check boxes next to each let you toggle the select permission. Keep in mind that this extension isn't for casual enthusiasts. Disabling permissions can prevent an app from functioning properly. A gaming app that wants your location data may seem strange at first, but it's possible that the game has a legit reason for the request, such as finding other players that are nearby.
Another problem with the extension is that the developer freely admits that it's in rough shape as it now. As the instructions on the download page indicate, sometimes it breaks sites, but it requires a certain degree of savvy to even install. You must be comfortable creating a git clone of the extension repository and working with Google Chrome in developer mode, since the more usable public build of the extension isn't ready yet.
Along with a better name and look, and a standard installer, Selph says that he is considering other options for future versions, such as allowing people to add permissions that an app hasn't requested. That might be the first time in the brief recorded history of Facebook that anybody has expressed the desire to give Facebook apps more access than they already have.