I don't recommend an upgrade because some programs that are not supposed to work with Vista might pretend to work if they were installed before the upgrade. With that said, I know that ProntoEdit works just fine on a clean install of Vista.

[Link: remotecentral.com]

I have an upgrade DVD. You cannot do a clean install with the upgrade DVD. But there is supposedly a workaround. There were rumors circulating that if you don't put in your CD Key until after you finish the install (leave it blank when setup asks for it) that you could add the key after Windows loads for the first time. I've tried this and it doesn't work. However, I read on Computerworld the other day that to pull off a clean install you should follow the procedure above but don't put in the key after Windows loads the first time and don't activate. Instead, run Vista setup again and upgrade the new install of Vista. Apparently this time it will let you use your Upgrade CD Key. I haven’t been able to test this.
I pulled off as clean of an install as possible (knowing what I knew at the time) by doing a clean install of Windows XP SP2 then immediately doing the upgrade. I did the custom install and told it to copy my files to C:\Windows.old.