[Strictly speaking not an application, but since we can get it through Installer, it's probably in the right place here.]
In November, TUAW reported on the settings you don't see in the Settings menu. There are a lot of them, including the tilted reflective dock, the numerical value (instead of an icon) for network strength and battery level, replacing the time with your name, etc.
A few weeks later, they also discovered how to modify the Settings menu to include these preferences: see http://www.tuaw.com/2007/12/18/tuaw-...tings-screens/
This was nice (I used it to add "Shuffle by Album" to my settings), but a lot of work.
Now someone named BlackWolf has done the hard work and added virtually every hidden setting you can think of to his Settings menu. It's availbale for download through Installer. He's added some twenty things you can set, and changed the organization quite a bit. See this blog post for an overview. Whether you like it depends on taste. You can completely undo it by uninstalling the tweak again through Installer.
To get this, you add the BlackWolf Repository in Installer (at the Sources, press Edit and then Add http://m8an.de/installer.xml ).
Then you will find the application Advanced Preferences (iPhone) in the Tweaks category.