What is the best way to understand what is going on in Windows Registry? Is there a book that can help you learn?
The system internals tools are excellent for this. You can download regmon free of charge and then you can see all the access that occurs in the registry.
I learnt about how it all works by reading a book about Windows95 and the registry, but it should also be covered in Windows Internals what can I say but Mark Russinovich is a god when it comes to this stuff.
The registry is a storage mechanism, which is used both by MS Windows itself and third party app developers (e.g., Adobe). Microsoft uses it to store user preferences, many of which can be controlled via the user interface (e.g., Control Panel settings, network connection settings). Application developers usually use it to store similar things.
Sometimes, you can bypass limitations in a program's user interface by changing settings in the registry directly.
Watch Russinovich's videos. I've spent about 4 hours on them this week and they are pretty fascinating.
There doesn't appear to be a book for Vista, but here's one from Microsoft Press for XP called Windows XP Registry Guide. Not too much is different in Vista. http://www.microsoft.com/mspress/books/6232.aspx Best to get your info from the source, right?
And, of course, the Wikipedia article is very comprehensive, but it's rough reading. http://en.wikipedia.org/wiki/Windows_Registry