Well if you do that then you're doubling the amount of files on your iPod. You have the ones you can play and the ones you can access in a seperate folder. If you have the space, go for it. Otherwise I'd invest in an external hard drive and save yourself time and grief should your computer crash
if you're running Mac OS X 10.6 [[I'm sure you can do it with previous versions, but 10.6 is all I've worked with]] then there is a program called Time Machine. Get an external hard drive [[I'd work with Western Digital but if you have the funds go with LaCie]] and plug it in. Then open up Time Machine and follow the instructions it gives you. From there you can schedule backups, how often to do it and so on.
If you're running Windows 7 there is a program or option [[probably on the control panel]] called Back Up and Restore. Use that the same way I mentioned before. Plug in the hard drive and then follow the instructions.
If you're running Windows Vista then it's the same thing as Windows 7. Go to the control panel and click on Backup and Restore Center.