I second what superlarry said. I have done both many times and a clean install is always better...faster...the System always performs better. I make all all kinds of promises that I have learned to keep about not installing a lot of third party apps. I now have a mouse driver, and that's it for thrird party pref panes. A package for loading mysql, FrontBase for WEbObjects and in /Library/StartupItems. Bells and whistle are interesting, but they all take some cycles and affect performance.
I have a good back-up/archive strategy that I've devloped over time because I get developer seeds and have to re-install frequently. Clean install start to finish with 95% of apps and functions restores takes about 3 hours.
Craig