Nope..it upgraded fine for me. Kept all my applications, settings, etc. I've had it for a week and I've only run into one problem, Fraps doesn't seem to work for my games. Doesn't bother me too much though, since it's a minor problem.
I didn't have any problems either, although I did a clean install so I could keep my windows 7 and just have a dual boot with windows 8. And I did use the 39.99 upgrade download just in case you were wondering. Windows 8 does take some getting used to, but overall it is a nice experience.