1. Security
Keeping your computer and it's information secure can be a difficult job. Using good programs such as AVG Free, Ad-Aware SE, Windows Defender, Spybot Search and Destroy, and TuneUp Utilities will keep your computer free of any viruses, spyware, or malware, and can keep your computer free from any infectious files.

2. File organization
Yes, organizing your programs and other files is really important. Personally I like to use an alternative to the My Documents folder. Make your own folder with your name and sub folders such as, Games, Music, PDF, Pictures, Videos, Programs, Documents, Genesis (where you keep things you're making with programs like, dreamweaver, photoshop, etc.). This way, all your things are in one place so you can easily move things from your computer to a CD or share them on a network or at least know where you might find something.

3. Stuff organization
You definitely want to keep your computer things such as driver CDs, hardware and/or cables, or game CDs in one place. Use a shoe box and put it on top of your computer, that way, it's all in one place, you can take it places, and you don't lose any software or hardware you need.

Notes:
To keep CDs in usable condition, make backups, and if you have a large hard drive, you might want to get a program for making images of your CDs and keeping them on your hard drive for later use so you have an un-damageable CD you can mount on a drive using a program such as Alcohol 120% or Daemon Tools. You can use this method to play games without the CD, plus it reads faster than any drive available.

Your hard drives need care too so you might want to defragment your hard drive regularly, if you have multiple hard drives you might want to pick up Diskeeper. Also you might be able to use the power of google to obtain these programs.