While our upgrade experience was fairly good, we recommend that administrators opt instead for a clean install, teamed perhaps with Vista’s Windows Easy Transfer utility for carrying over files and settings from the previous install. Not only is a clean install much faster than an upgrade, our tests show, but the significant changes in how Windows Vista handles software installation bring the possibility of compatibility issues that might not be immediately apparent.
I have always thought this was common sense, but apparently not. Fresh install means a smooth running system. If after a fresh install you run into a problem, you can’t very well blame it on the fact of upgrading ;-)