I have recently talked with a lot of people that had to buy new copies of there games because of all the use and abuse we tend to put them through.
The best ways I have found to protect them is to NOT USE THEM AT ALL.
You can do this in one of two ways:
1) NO-CD Patch - That works great but they can be hard to find for many new games and there is always the risk of downloading more than you bargained for.
2) ISOs - This is a very good and safe way to use the games without loading the game disc. Simply make a "disk image" or ISO with a burning program. I use Roxio 7.5.
Keep your game ISOs in their own directory that will be easy for you to locate then you can use a virtual drive program to mount them and it is the same as having the game disk in your real drive. For this I use Alcohol 120%. I even keep my Key Codes on a Read_Me file I create with notepad in the folder with the ISO.
If you store the ISOs on a separate drive then you can use them to install the games in the event you have to format. That works equally well on ANY program that you install with a disk!
;D
Oh BTW, if you have more than drive or just one that is partitioned off then why not keep your game installs there? The reason I say that is I format quite often because NOTHING beats how a machine runs on a fresh install!