Where does iTunes store my iPhone and iPad backups?

Where does iTunes store data for iPhone and iPad backups? I know that—on a Mac—the following folder is ostensibly the only location.

~/Library/Application Support/MobileSync/Backup

I actually replaced this with a symlink to an external hard drive to free up space on my laptop, and was thus a bit surprised to find that backing up my iPhone nevertheless continued to decrease the free space on my laptop's hard drive. I eventually discovered that the following folder was the culprit.

~/Music/iTunes/iTunes Media

Are there any other folders that iTunes uses for its backups?

Mobile applications (.ipa files) are stored in the following folder and can take up a lot of space:

~/Music/iTunes/iTunes Media/Mobile Applications