I'll tell you what I just did recently. I put in the FS2 discs, opened up My Computer, right clicked on the DVD drive and selected Explore. This opened up all the files in the disc. I then copy and pasted all the files to a new Folder I created like so: My Documents\Freespace Folder\Freespace 2\Disc 1 And I put them all in there. I then did the same for disc 2 and 3. Then I also put all of the contents of my Freespace on discs in the Freespace folder for disc 1, 2, and Silent threat.
After that, you can install the retail version of the game completly without using the CD's. I would just open up disc one and douple click on the setup icon (it looks like a picture of a computer). Install will run normally. When it asks you for disc 2, you click on Browse and go to My Documents\Freespace Folder\Freespace 2\Disc 2, and so on for Disc 3. Do the same for FS1 and Silent Threat.
Now you don't have to worry about your discs getting scratched up. You now have a back up of your discs and you don't have to worry about them getting scratched beyong repair or lost. Burn the files in these folders to a CD so you don't have to worry about losing info on your hard drive in case something happens.
This will not play the cutscenes, even if you burn an exact copy of the FS2 discs and have it in the drive. You'll need FSOpen to play them. Read
Karajorma's FAQ so you can learn about how to do so.