Just so you know, Mac OS X is a Unix OS which means there is no registry (thank God). All the configs are saved as files in ~/Library/Preferences for your own settings, /Library/Preferences for global settings, or in another location specified in the README file for any application if not in any of the aforementioned locations.
Also, Unix operating systems tend to defragment their hard drives when they need to automatically. You don't have to tell it to defrag.
What you might want to do it boot from the install discs and have it repair the HD by calling Disk Utility from the menu. You can also do what's called a repair on permissions when booted into your Mac OS X system that's already installed. Just head to Applications-->Utilities and launch the installed Disk Utility app and run the permissions repair.
There's also a third party app called
OnyX that is very recommended for disk maintenance like cleaning out old files and whatnot. Just be sure to download the version that is appropriate for your version of OS X.