OS X has roots in Unix, and the Library folders relate to that.
Because both Unix and Mac OS X are MULTI-User operating systems, certain things are specific to individual users. Things like desktop backgrounds, email account settings, preferences for specific apps. These live in your Users' folder (~/Library is the shorthand for saying /Users/<your username>/Library).
There are a set of global library items that apply to EVERY User of the system. These are things like global serial numbers for Apps (so that Photoshop, for instance, can be used by every user on the system). There are other settings and things that apply globally too. These are in the /Library folder. It is here that all third-parties are expected to put their library-type settings.
The /System/Library/ folder is where Apple stores all their library-type information. It is essentially restricted for their use and contains most of their "secret sauce" frameworks and private programming that they do NOT document for developers.
The reality is that all these libraries are editable by you, the end-user Administrator, but that messing with the content of Library folders other than your own ~/Library folder (and even that is to be taken on with caution) is not wise for a non-Unix-geek.
The Mac OS X does not have a central repository for its information like the Windows Registry. Prefs are generally kept in separate files and referenced directly by the entity or app that needs them. This is different from the unified database in Windows in that there is no "database" to become corrupted or which requires an app to edit or modify per se.
The subject is deep, and I am just skimming the surface. I hope this helps.
