Is there a way for my iPhone app to add media (mp3s) not in its iPod library to iTunes once the user plugs/syncs to a desktop such that the media will get sync'd back into the iPhone's iPod library?
I know the question is rather general, but if it is indeed possible, can anyone nudge me in the right direction?
No, it's not possible to do this using anything provided by the iPhone SDK. The only way to do something similar would be to store the media in your iPhone application's local storage, write an OS X application that discovered your iPhone via Bonjour, synced the content via WIFI, and then added it to iTunes.
Take a look at "Things" (an iPhone todo list application) if you'd like to see an example with sync-to-desktop functionality.
Who wants to write a sync app for mac and windows? Try serving a bonjour discoverable upload page from the iPhone. I got cocoahttpserver up and running in a few minutes.