Well, I know GNOME project uses something similar to the registry for holding configurations settings for much of it's GUI.
It's not realy like the registry, I beleive the information is kept in the form of xml-based (think so) configuration files, which are esentially ascii plain text files vs the binary strings and keys that make up the windows registry.
For your user configurations all the config files are stored in .filename files and directories in your user's home folder. That way everything is in your home folder and their isn't any need to give your users rights out side of that. The rest of the OS can be completely read-only (well that + the executable rights for programs)
The . before the filename makes the file "hidden" so that it's out of the way for normal use. "ls" won't show it, but "ls -a" will.
That way it's nice because if any program geeks out and writes a unusable configuration you simply delete it's file or folder and it is regenerated with default settings next time you start it up.
There are a few usefull things you can do by editing the Gnome's registry-like settings, like turning off "spatial mode" (which I am a fan of), and making "explorer mode" the default for nautilus.
Mozilla/Firefox has something similar were you can edit it's special configs by typing about:config
Anyways, most "gnome" apps don't use the gnome "registry" very much, most programmers prefer to use their own .dirname or .filename type configurations. But it's fun to mess around with if your a tweaker, worst thing that can happen is that you would have to delete the .gconf directory, which I think is were it's stored (not completely sure).
I am pretty sure that's what the "registry editor" is for, gconf, but I'd never messed with it so I am not completely sure.
edit:
here is a page for gconf.
They make a distinction between "user preferences" and "configurations". This is for "user preferences" only. System wide configurations, of course, are stored inside the /etc/ directory, and rarely inside some of the subdirectories in /usr/ and /var/. Which are completely unaccessable to users.
So you can freak out on gconf all you want, and not worry about it screwing up anything outside of your user preference's, so it's not like Windows were one false move will render your system unusable.