several problems I can already foresee here.
First, I know you won't like it, but I am going to blame this on using the MSN browser. Really.
Second, backing up many programs by copying the files to a CD or other hard drive won't cut it. They will have dll files in other directories (usually the C:\Windows directory). Some programs run just fine with the files in their directory, but most larger programs (like office suites, graphics programs, etc) require registry or dll files elsewhere to function. There's not really a way to trace these without researching each program individually and finding o ut if anyone out there has documentation on what dlls are needed and what registry information needs to be corrected.
As for your documents, do a search for .mp3, .doc, .jpg, .gif, .tiff, .png, .xls .txt, and .htm* files. Scan through the list on many of them to see if they are things you'll need (many programs use these files for other things, so you may not need all of them). Check the file path if you don't recognize the name of the file to be sure it's not something you made or were sent. There may be other file extentions you're interested in saving too (Keynote uses a .knt file, for example).
make sure you back up your email and export your bookmarks and save that. Also remember any saved games you want to keep and any programs that use separate preference files (SecureCRT, mIRC, etc).
I try to make backing up my hard drive easy. I specify that my email programs use a subfolder of My Documents to store email. Whenever I install a program I go through the preferences to see if there is a separate preference file, and I save that file in a My Documents subfolder as well. Any file I download is saved to a My Documents Subfolder (including stuff gotten over Trillian or mIRC, where I can specify the default download directory). Any file that can be used a different computer goes somewhere in the My Documents folder. I keep it very organized. That means when I back up I back up three things: My Documents, Saved Games, and bookmarks.
DON'T use the desktop as a storage location, that is lazy.
One last thing, what Windows are you using? and if it's 2k or XP, do you know what file system you are partitioned to? If it's FAT/FAT32, you can put in a DOS disk, boot to that, and manually delete all those files. If you are partitioned using NTFS (if you are using Windows, you will have partitioned using either FAT or NTFS), there is also a command line you can reach from a) the 2k/XP install disk or b) booting to safe mode both of these are a little more restrictive about how you can do it, and they don't use the exact same commands as DOS. Go to bootdisk.com if you need to make a bootdisk.