Correct way of Shutting down Virtuoso server

Here is the correct way to shut down the virtuoso server.
At the SQL prompt type SHUTDOWN. This is the normal way of shutting down the virtuoso server.
For virtuoso in particular killing the virtuoso process would result in all transactions since the last checkpoint not being comitted to the database and remaining in the transaction log file, which would then have to be replayed when the server is next started. Whereas performing a normal shutdown will automatically run a checkpoint to commit all outstanding transactions to the database before shutting down.

For more information read at http://docs.openlinksw.com/virtuoso/isql.html#invokingisql