The Microsoft Exchange Transport service is a service available both on the Microsoft Exchange Server 2007 Hub transport server role, and Edge transport server role.
This service is the one responsible for sending mails to their final destinations, and stores those messages and items belonging to the transport dumpster in an Extensible Storage Engine database by default called Mail.que.
When you stop the Microsoft Exchange Transport service, Exchange will no longer be able to accept new messages, and Exchange will not continue to deliver existing queued messages.
By pausing the Microsoft Exchange Transport service on the other hand, Exchange will allow existing messages to be delivered, but will stop accepting new messages.