I have recently setup a second "CRM organization" for a client, to manage their construction projects with Dynamics CRM 2011.
In the final stages of deployment, I had a brain-fart when configuring the email router for the second CRM organization. Their first installation instance of CRM was ticking along, happily sending out emails. The new instance, just had the emails sat 'pending'.
After some basic setup confirmation, the problem was that the user account being used for checking & sending mail with exchange, was not a CRM user in the new organization instance.
Once, I had added the user account to CRM, it sent all the pending emails and my inbox started chirping 'new mail'!
Thanks to this InteractiveWebs Tech Support article.
The account that is specified in the Access Credentials field on the General tab of the E-mail Router Configuration Manager must be a Microsoft Dynamics CRM administrative user. If the access credentials are set to Local System Account, the computer account must be a member of the Active Directory PrivUserGroup security group.