Other reasons to have multiple databases. We have one application that everyone can access. We also have client database that are very differnt from client to client. It is easier to maintain the application that all clients use (and which is maintained by a differnte team) if the client_specific data is separated out to their own databases. It is also easier to move the client to a new server when they become a large enterprise client rather than the smaller clietns who run on a server with many other clients.
Further there are types of data that are transactional and need to be in databases that are set to full recovery mode with full transaction logging. Other data is only populated from imports and does not need transactional logging and which might slow down the system as the log grew enough to handle the 10,000,000 record import. These are often split out to a separate databse so they can be in simple recovery mode as it si not necessary to recover data from the transaction log if there is a problem, it can be easily recoverd by re-running the import.
Then data is split out into datawarehouses which are optimized for data reporting not transactions. Again these reporting databases are usually separate databases (often on separate servers).
Then you have the databases for multiple different COTS applications (we have accounting databases, Credit Card transaction porcessing databases, HR databases, our project management database). A particular website might need to access more than one of these or transfer information from one to the other. Believe me vendors won't let you copy their database structure into one database to rule them all.
We have several hundred databases here on many differnt servers.