This is a neat way of cleaning the gnome registry, useful after an upgrade or if you simply want to speed up the machine.
apt-get install gconf-cleaner
Remember to first back up in case anything goes wrong:
cp -av ~/.gconf ~/.gconf-backup
run gconf-cleaner
It showed about 1200 keys in my system that could be cleaned.
Yes to all.
Check this tutorial out, great visuals:
http://www.linuxinsight.com/how-to-cleanup-your-gnome-registry.html
U8UNTU eLXER 
I just tested this tool and it did not work as advertised. It only wanted to remove entries for applications I still have installed. In most cases this would have just reverted the apps back to their default state. Not harmful, but annoying. Gconf-cleaner doesn’t remove the “left over” entries that you see in gconf-editor in the left hand pane — the ones you can’t right click and delete. Which are probably the ones people are looking to get rid of when they use this tool.
If you’re concerned about left over stuff when you remove an application, generally you only need to delete the dot directory in your home directory. (e.g., if you remove, “myapp,” you can delete ~/.myapp and be done with it.) Your package manager intentionally leaves these directories because they contain personalized settings and things of that nature. Left over gconf stuff is in ~/.gconf/apps/myapp, which can also be deleted.
All of this will still leave the non-right-clickable entries in the left-side pane (which again gconf-cleaner won’t fix, either). If you REALLY want to get rid of those, I believe you can edit the xml file that gconf-editor is a front-end for: /etc/gconf/gconf.xml.defaults/%gconf-tree.xml
Within that file, remove the xml info for the entires you want gone. Make a back up before making changes. Like this:
dir name=”myapp”>
possibly some stuff here
/dir>
You’d get rid of those lines anywhere they appear (usually twice). Then restart Gnome.
Finally, it should be noted that the gconf entries, as mentioned above, are stored in xml files. This is nothing like the Windows “registry.” Cleaning what you see in gconf won’t free up more than a few bytes of disk space, and absolutely will not increase system performance. The only reason to do this is because it really bugs you when you’re in gconf-editor and see excess entries on the left.