You need to back up the saved game folders. They are are a bugger because they are not always stored in the same location. This needs to be standardised really. Some you can locate these by right clicking on the game in the game browser others you'll just have to do a search..
For example, COD MW1 - For Vista/Win7 it's C:\Users\YOUR PROFILE\AppData\Local\VirtualStore\Program Files (x86)\Activision\Call of Duty 4 - Modern Warfare\players
for MW2 - C:\Program Files\Steam\SteamApps\common\call of duty modern warfare 2\players
When you reinstall the game, just copy back to the same location.