Is there an iPhone app available that lets me track data usage on a per-app basis?
Since version 4.3.0 of "My Data Manager" (see screenshot) that app does not track usage based on which app that use the data. According to the version description it was due to a change in the App Store guidelines.
If "My Data Manager" had to remove the feature I assume that all other apps also have to remove it.

If I remember correctly it was something about not showing other developers apps in your own app, but I could be wrong.