Your home folder contains several organizational folders. They are Desktop, Documents, Downloads, Library, Movies, Music, Pictures, Public and Sites. Of these folders, you should only save documents to your Desktop, Documents or Public folders.
- Desktop Folder. The Desktop folder in your home folder is the same as the Desktop that you see when all windows are closed or by using Exposé (Command-F3 on new keyboards, F11 on older ones). It is meant for temporary storage of files. I've seen Macs with hundreds of documents on the Desktop, but it that is very messy and can even slow down your Mac.
- Documents Folder. This is the place to store all of the documents you want to save long term. You can create folders inside of the Documents folder to further organize your work. Most applications will default to the Documents folder when you go to save for the first time.
- Public. Any file you place in the Public folder is visible to other users. It is useful for sharing files with other users on the same computer.
You should stay out of the other folders in your home folder. They are used by specific apps and you can mess things up by poking around in them.
- Library Folder. The Library folder stores information needed by your Mac and your apps. Unless you really know what you are doing, you should stay out of this folder
- Movies folder. Projects you create in iMovie get stored in the Movies folder. iMovie manages the contents of the Movies folder and if you move files around in there, iMovie can get confused. (Note: If you take movies with your digital camera, these movies will end up in iPhoto. Work with them from inside of iPhoto.)
- Music folder. The Music folder holds your iTunes Library. Since you do all of your importing and purchasing of music in iTunes itself, there isn't any need to wander into the Music Folder.
- Pictures folder. The Pictures folder holds all of the photos from iPhoto and Photo Booth. Both of these applications use their own system of organizing their files and no good at all will come from trying to figure it out.
- Sites folder. iWeb stores its files here. Like the other folders to stay out of, iWeb manages the contents of this folder and you should not disturb its organization.