IPhone Apps - Where Is User Data Stored?

Where is the user data associated with an iPhone app stored? Is it stored within the app's .ipa file? For example, I use Weightbot. Is all of my personal data stored within the Weightbot.ipa file, or is it stored elsewhere?

The reason why I bring this question up is, I've somehow lost 1GB of storage from my iPhone 3GS!
I've added up the data size of all the apps on my iPhone. I've got 61 apps in total, which take up 1947.38 GB of storage. However, the Capacity bar in iTunes is telling me that my 61 Apps are taking up 3.10 GB!
So, somehow I've lost over 1GB of storage on my iPhone. How can that be?

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