"Empty Trash" removed other files.

This is rather frustrating, since I just received my MacBook Pro yesterday. I transferred a number of files off of my old laptop to a folder I created on the desktop, via USB Flashdrive. Also, I have a Creative Zen Micro that has all my music on it, and so I used the 3rd party program XNJB to access it and retrieve the music. Instead of putting the music into the Music folder, it put all of it into the Applications folder. After copying it all into the iTunes library, I removed it from the Applications folder, and cleared the trash. That not only cleared the trash, but also removed the folder I had created on the desktop, as well as the Music, Pictures, Movies, and Documents folders. I tried reinstalling using the reinstall discs, but to no avail. Help?
MacbookPro   Mac OS X (10.4.9)  

I suppose I should make a clarification. The help I'm looking for is how to restore the folders to the Library. The files are of no interest, as they are easily re-transferred

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