* Sounds
* Services
* Visual Effects Settings
* Device Drivers - Be sure to have these handy to reinstall. They do not always remain after the repair (upgrade) install.
* You may lose the ability to sign on to MSN Messenger, to solve this problem have a look at this thread Unable to sign in to WLM.
* You may lose your custom themes due to not having permisions set on the old themes. Go to the hidden themes folder at C:/Users/(User-Name)/AppData/Local/Microsoft/Windows/Themes, then Take Ownership of the themes folder and you will now have all your themes back.
* It has been reported that you may also lose your Media Center gadget after doing the repair install.
* Windows Updates will need to be checked and reinstalled again.