I'm not sure I understand the specific complaints in the post. The metadata in iTunes is stored in a standard way, attached to the audio files themselves. All the playlists, repeated track infromation, etc, is stored in an XML file with simple structure. This should be as easy to convert as if the music database had been stored anywhere else.

Similarly, for iPhoto, much of the metadata is attached to the photos themselves. The album information is in very simple XML. I'm not sure how the cropping, rotation, etc, are stored, but the final JPEG can be exported from the UI, and nearly all these applications are highly scriptable.

Storing data in any application results in some restrictions in how that data can be transformed and/or used in the future. The iApps use fairly transparent data formats that are accessible to pretty much any programmer. I'm not sure if there's any open source alternatives to these apps that make it much easier to pull out data. Putting data in these apps is not mortgaging your future as much as putting your documents in MS Office format, for example.