You only reinstalled the Operating system directory. So all of your old programs are still in place but when you launch them you get error messages? Thats because your registry was replaced when you "reinstalled your operating system" your operatings system doesnt know where your program files are because your registry doesnt know where they are.
I have only done "reinstalls" like this if there is data i need to backup (pics, music, doc files) before i do a format-install. Your going to end up doing the same amount of work (reinstalling software) anyways after a reformat.
In the end it is less "painful" if you just format your harddrive and resintall your software. you can keep your computer as is and keep reinstalling software but it can get confusing if your looking in your doc & settings folder, plus you will probably face problems down the line. Your registry should always reflect whats actually on your computer