As a general rule in the IT industry we generally advocate clean install vs upgrade, however when it comes to my home PC I can be lazy at times. I decided rather than doing a clean install I would upgrade my PC from Windows Vista Ultimate to Windows 7 Ultimate. I ran through the upgrade process and was immediately impressed with Windows 7 and disappointed with some weird issues my computer started having immediately after the upgrade.
1) Any time I opened an application (any application) the PC would free for about 4-5 seconds
2) After any reboot my Internet connection would not work unless I went into device manager and uninstalled and reinstalled my NIC
I attempted to troubleshoot the isssue to no avail. In the end I wiped the thing and did a clean install of Windows 7 and now everything runs beautiful.
So to answer the question of upgrade vs clean install, always do clean install. Really, I should have known better.