[macgirl]

In iTunes, you should now have an Applications entry in the Library Source list on the left - this is where you can see all of the apps you have downloaded from the App Store. Technically, it's stored in your iTunes Music folder on your PC. I have a Mac and I'm guessing the file structure is different than it is in Windows when it comes to how iTunes handles this, but I have a Mobile Applications in my Music folder where all my apps are.

Don't move the apps around on your hard drive or anything - all installation and upgrading is done through iTunes automatically and moving apps will only confuse it.