Once I had multiple websites which got popular over time. They used separate databases, mostly because the hosting provider allowed only 1Gb storage space each. But! As soon as I released a service that included all these websites, I started having to do transactions amongst these websites, and the most convenient way to do this is definately moving everything into one big database.
So I optimized the database structure and squeezed the relevant parts to this central database, but left everything else out.
My opinion is somehow related to the paradigms of OOP. Similar data must be stored together, so if you build different applications, you should use different databases for them.
In the above case using common db couldn't be avoided, but remember that I also kept some tables apart in a separate db, that aren't part of the common queries.
Moreover, if you keep them separated, they will be easier to backup, there will be less chance for data loss. If something goes wrong and applications interfere with each other, the database gets messed up, and you basically don't want to expose your app to this danger.
All in all, you can maintain a common database for common queries, but also keep one for each of your applications.