Having started as a music player, Apple's iTunes application has historically organized content in your account's Music folder. With the introduction of iTunes 9, Apple applied slight changes to the default organization of files that iTunes manages, which may or may not show up for you, depending on how you use iTunes.
Before iTunes 9, the program kept music files in the "/username/Music/iTunes/iTunes Music" folder if you have enabled iTunes to organize your music files for you. When Apple included the ability to play video files, these were also stored in this folder under subdirectories for "Movies" and "Podcasts," among other categories. If you downloaded games and applications for your mobile devices, these were kept outside of the "iTunes Music" folder, in their own separate folders.
With iTunes 9, however, Apple changed the default name of the media folder to "iTunes Media" instead of "iTunes Music," and included all items that iTunes manages in this folder in respective subdirectories. While this is the default setting for iTunes, if you started with a previous version and then upgraded to iTunes 9, the program has kept your previous organization scheme. However, if you use the iTunes store to download new content, the new items may be stored in the new scheme, with iTunes just maintaining your old organization.
This may be particularly apparent for people who have kept their music in alternative locations, such as external hard drives. iTunes will keep the music on the external drive as it is organized, essentially allowing you to organize it yourself, but if you download new content it will put it in the new "iTunes Media" default locations.
While this may not be too important to most people, it might cause some confusion for people who store their iTunes content in locations other than the default /username/Music/ folder. To ensure iTunes 9 keeps your files where you want them, go to the "iTunes Music" folder location and change the name to "iTunes Media", and then in the iTunes preferences under the "Advanced" tab click the "Change..." button and choose the newly renamed folder. Then ensure the options to keep the media folder organized, and to copy files to the media folder are both checked.
If you are still using the old organization scheme for iTunes, you can easily upgrade to the new one by choosing the "Organize Library..." option in the "Library" submenu of iTunes' "File" menu.