Personalization
These applications basically will reveal hidden functions of Finder, Exposé, Dock, Safari, Spotlight and other global preferences. They increase OS X’s functionality and allow you to modify your system to suit your needs; and eliminate settings that you don’t particularly enjoy.
Deeper and
TinkerTool
Both of these applications are pretty much alike. They perform the tasks mentioned above and a few more. TinkerTool, for example can disable the creation of .DS_store files on network drives, fix the Dock so that no changes can be made to its content and add a stack for Recent Items, even change the Dock to give it a 2D look in Leopard. There are also more advanced options like how an application crash is handled and enabling developer modes for Safari and Dashboard.
Secrets
Secrets is different because it is actually a preference pane which allows you to tweak a lot of settings through System Preferences. The full list of what you can do with Secrets is found here, it is so long it’s exhausting to read! But you get the gist, almost any setting can be tweaked.
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