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In my current desktop and laptop i run:

Nepomuk (with embed mysql)
Korganizer (with embed mysql)
Amarok (with another embed database)
Digikam (with another embed database)
Marble (i read somewhere that it will use some database)
...

Having so many embed databases seems a waste of resources and makes it more complicated to backup my workspace to another machine.

Why not focus on using a single KDE based database and abstract all datasources from these and upcoming apps to use this datasource?

As far I know, Nepomuk can be set to use external database.
KOrganizer uses Akonadi and it can use External.
Amarok and digiKam (check spelling) can have external MySQL.
For Marble I am not sure. But you can have only single MySQL database running.

Why we do not use one single MySQL? Because it is not installed by default in all distributions and having a depency to server what takes more resources than multiple internal databases is not wise as well.

The MySQL setup is not so easy that normal user could do it. What we really should get is that user could just see from one place that what applications are using as database. Then just link them to use one. No hassling with database setups, automatic backups and system recovering for full database systems etc etc.