You would have to re-install all of your games and app's there is really no way around that. Steam being one of the exceptions while you will have to re-install the application as long as you do not delete the SteamApps folder and everything within that folder you will not have to download your games again. Depending on the amount of games if you have Steam could save alot of time I know my Steam account comprises almost 2tb in size and takes a full day to re-download.
If you are having that many problems with Windows I would bypass a repair install and go for a complete format and re-install. I know it can be a pain but if you can get all of your drivers and such downloaded before hand that can save some time by having everything ready to go.