I'm wondering if there is something that would give the user more fine-grained control of preferences? Something like "TweakUI" and the other Power Toys on Windows.
There are a number of options for this that tweak basic hidden preferences and have several small UI tweaks built in. None of them have very substantial UI tweakery though.
Most of these have the same basic tweaks because they are simply enabling/disabling hidden preferences.
Cocktail - Has a number of hidden tweaks (including UI) in a simple application.
If you are looking for something more similar to a styling application, there are a number of themed programs which will completely change the look.
If you don't know about it already, you should look at CandyBar which makes basic dock changes and icon styling dead simple. MacThemes has a number of excellent posts and threads on UI tweaks and themes that you might be interested in.
Titanium has an application called Deeper that allows some tweaking, however there is not a lot you can tweak compared to Windows. Mac is mainly focused at being simplified and easy to use.
There is also a System Preference plugin that you can use for tweaking but I can't recall what it is called at the moment. Will update.
VersionTracker has a category dedicated to tweaking MacOSX applications as well.
As a general all-round customisation tool, my vote goes to MacPilot, as menitioned by @bjtitus. The most common UI tweaks (displaying hidden files etc) are available, along with a load of other good stuff.
There is an article on MacWorld magazine here that has some other good info and recommendations that might help.
Of course, the CLI